# HG changeset patch
# User metaboflow_cam
# Date 1571732371 14400
# Node ID 55efed82d7ecb7c22a11953abad8acf7a00d50c5

Uploaded

diff -r 000000000000 -r 55efed82d7ec lcms/README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/README.md	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,50 @@
+# LCMS for Galaxy #
+
+Galaxy tool for LC-MS data deisotoping and annotation for metabolomics
+analysis.
+
+
+The original codes by Zoe Hall is located in 
+[lcms_processing](https://github.com/hallz/lcms_processing_). 
+
+## Installation ##
+
+- Install [Galaxy](https://github.com/galaxyproject/galaxy) under Linux.
+
+- Install [conda](https://docs.conda.io/en/latest/miniconda.html) under
+  Linux. `conda` is used to install `requirements` of this tool, i.e. R
+  packages used: `optparse` and `xcms`.
+
+- Use `git` to clone this tool
+
+  ```bash
+  git clone https://github.com/wanchanglin/lcms.git
+  ```
+
+- Add this tool's location into Galaxy' tool config file:
+  `~/Galaxy/config/tool_conf.xml`. For example, one simplified
+  `tool_conf.xml` looks like:
+
+  ```xml
+  <?xml version='1.0' encoding='utf-8'?>
+  <toolbox monitor="true">
+    
+    <section id="getext" name="Get Data">
+      <tool file="data_source/upload.xml" />
+    </section>
+    
+    <section id="MyTools" name="My Tools">
+      <tool file="/path/to/dimsp/lcms.xml" />
+    </section>
+
+  </toolbox>
+  ```
+
+- Test data are in `test-data`.
+
+## Authors, contributors & contacts ##
+
+- Wanchang Lin (wl361@cam.ac.uk), University of Cambridge 
+- Zoe Hall (zlh22@cam.ac.uk), University of Cambridge 
+- Julian L Griffin (jlg40@cam.ac.uk), University of Cambridge 
+
diff -r 000000000000 -r 55efed82d7ec lcms/lcms.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/lcms.R	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,359 @@
+#' wl-12-03-2018, Mon: Commence
+#' wl-15-03-2018, Thu: Tidy R codes
+#' wl-19-03-2018, Mon: Use Zoe's parameters setting for 'xcms'
+#' wl-20-03-2018, Tue: Use 'peakTable' to get peak list
+#' wl-21-03-2018, Wed: Major changes
+#' wl-23-03-2018, Fri: Test and debug deisotoping and annotating
+#' wl-26-03-2018, Mon: Minor changes
+#' wl-17-05-2019, Fri: modification for Galaxy
+#' wl-21-05-2019, Tue: use 'makelibrary' from 'massPix'
+#' wl-22-05-2019, Wed:
+#'   - compare deisotpe and annotate with 'massPix'
+#'   - move adducts into annotate function
+#'   - run in interactive mode
+#' wl-23-05-2019, Thu: Fix some bugs.
+#' wl-24-05-2019, Fri: debug
+#' wl-28-05-2019, Tue: retcor
+#'  - 'retcor' consumes a large quantity of memory by 'profStep' and
+#'    disable its plot.
+#'  - use average of all samples' intensity for deisotyping
+#' wl-30-05-2019, Thu: add 'samp_name' especially for galaxy
+#' wl-14-10-2019, Mon: fix a bug for planemo test only. 'planemo test' will 
+#'  put 'test-data' in an random directory. To avoid this, use 'samp_name'
+#'  directly in 'peaklist'.
+
+## ==== General settings ====
+rm(list = ls(all = T))
+set.seed(123)
+
+#' flag for command-line use or not. If false, only for debug interactively.
+com_f <- T
+
+#' galaxy will stop even if R has warning message
+options(warn = -1) #' disable R warning. Turn back: options(warn=0)
+
+#' ------------------------------------------------------------------------
+#' Setup R error handling to go to stderr
+#' options( show.error.messages=F, error = function (){
+#'   cat( geterrmessage(), file=stderr() )
+#'   q( "no", 1, F )
+#' })
+
+#' we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+suppressPackageStartupMessages({
+  library(optparse)
+  #' library(WriteXLS)
+  library(xcms)
+})
+
+#' wl-28-08-2018, Tue: Convert a string seperated by comma into character vector
+str_vec <- function(x) {
+  x <- unlist(strsplit(x, ","))
+  x <- gsub("^[ \t]+|[ \t]+$", "", x) #' trim white spaces
+}
+
+## ==== Command line or interactive setting ====
+if (com_f) {
+
+  #' -----------------------------------------------------------------------
+  #' Setup home directory
+  #' wl-24-11-2017, Fri: A dummy function for the base directory. The reason
+  #' to write such a function is to keep the returned values by
+  #' 'commandArgs' with 'trailingOnly = FALSE' in a local environment
+  #' otherwise 'parse_args' will use the results of
+  #' 'commandArgs(trailingOnly = FALSE)' even with 'args =
+  #' commandArgs(trailingOnly = TRUE)' in its argument area.
+  func <- function() {
+    argv <- commandArgs(trailingOnly = FALSE)
+    path <- sub("--file=", "", argv[grep("--file=", argv)])
+  }
+  #' prog_name <- basename(func())
+  tool_dir <- paste0(dirname(func()), "/")
+
+  option_list <-
+    list(
+      make_option(c("-v", "--verbose"),
+        action = "store_true", default = TRUE,
+        help = "Print extra output [default]"
+      ),
+      make_option(c("-q", "--quietly"),
+        action = "store_false",
+        dest = "verbose", help = "Print little output"
+      ),
+
+      #' processing mzML or mzXML
+      make_option("--process",
+        type = "logical", default = TRUE,
+        help = "Select TRUE to process mzML or mzXML files by xcms
+                otherwise use the processed xset R data file"
+      ),
+
+      #' input files
+      make_option("--mzxml_file",
+        type = "character",
+        help = "mzXML/mzML file directory or full file list seperated by comma"
+      ),
+      make_option("--xset_file",
+        type = "character",
+        help = "xcmsSet R data file produced by xcms"
+      ),
+      make_option("--samp_name",
+        type = "character", default = "",
+        help = "Sample names. Default is the names of mz XML file"
+      ),
+
+      #' process raw data with mzML or mzXML format and get xcmsSet
+      make_option("--FWHM",
+        type = "double", default = 3,
+        help = "Approximate FWHM (in seconds) of chromatographic peaks"
+      ),
+      make_option("--snthresh",
+        type = "double", default = 5,
+        help = "The signal to noise threshold"
+      ),
+      make_option("--profmethod",
+        type = "character", default = "binlin",
+        help = "Use either 'bin' (better for centroid, default), or 
+                'binlin' (better for profile)"
+      ),
+      make_option("--minfrac",
+        type = "double", default = 0.25,
+        help = "Minimum fraction of samples necessary for it to be 
+                a valid peak group"
+      ),
+
+      #' make library
+      make_option("--ionisation_mode", type = "character", default = "positive"),
+      make_option("--fixed", type = "logical", default = FALSE),
+      make_option("--fixed_FA", type = "double", default = 16),
+
+      #' deisotope
+      make_option("--ppm", type = "integer", default = 5),
+      make_option("--no_isotope", type = "integer", default = 2),
+      make_option("--prop_1", type = "double", default = 0.9),
+      make_option("--prop_2", type = "double", default = 0.5),
+
+      #' annotate
+      make_option("--ppm_annotate", type = "integer", default = 15),
+
+      #' output files
+      make_option("--peak_out",
+        type = "character", default = "peak.tsv",
+        help = "Annotated peak table"
+      ),
+      make_option("--rdata", type = "logical", default = TRUE),
+      make_option("--rdata_out",
+        type = "character", default = "xset.rdata",
+        help = "xcmsSet R file after XCMS on mzML or mzXML files."
+      )
+    )
+
+  opt <- parse_args(
+    object = OptionParser(option_list = option_list),
+    args = commandArgs(trailingOnly = TRUE)
+  )
+} else {
+  #' tool_dir <- "C:/R_lwc/lcms/" #' for windows
+  tool_dir <- "~/my_galaxy/lcms/" #' for linux. must be case-sensitive
+  opt <- list(
+    process = F,
+
+    #' input files
+    mzxml_file = paste(paste0(tool_dir, "test-data/lcms_neg/ZH_180918_mann_neg_001.mzML"),
+                       paste0(tool_dir, "test-data/lcms_neg/ZH_180918_mann_neg_002.mzML"),
+                       sep = ","
+                       ),
+
+    #' mzxml_file = paste0(tool_dir, "test-data/lcms_neg"),
+    xset_file = paste0(tool_dir, "test-data/res/xset_neg.rdata"),
+    samp_name = "",
+
+    #' process raw data with mzML or mzXML format and get xcmsSet
+    FWHM = 3,
+    snthresh = 5,
+    profmethod = "binlin",
+    minfrac = 0.25,
+
+    #' make library
+    ionisation_mode = "negative",
+    fixed = FALSE,
+    fixed_FA = 16,
+
+    #' deisotope
+    ppm = 5,
+    no_isotope = 2,
+    prop_1 = 0.9,
+    prop_2 = 0.5,
+
+    #' annotate
+    ppm_annotate = 15,
+
+    #' Output
+    peak_out = paste0(tool_dir, "test-data/res/peak_neg.tsv"),
+    rdata = TRUE,
+    rdata_out = paste0(tool_dir, "test-data/res/xset_neg.rdata")
+  )
+}
+#' print(opt)
+
+suppressPackageStartupMessages({
+  source(paste0(tool_dir, "lcms_func.R"))
+})
+
+## ==== Pre-processing ====
+
+#' library files
+lib_dir <- paste0(tool_dir, "libraries/")
+
+read <- read.csv(paste(lib_dir, "lib_FA.csv", sep = "/"), sep = ",", header = T)
+lookup_FA <- read[, 2:4]
+row.names(lookup_FA) <- read[, 1]
+
+read <- read.csv(paste(lib_dir, "lib_class.csv", sep = "/"), sep = ",", header = T)
+lookup_lipid_class <- read[, 2:3]
+row.names(lookup_lipid_class) <- read[, 1]
+
+read <- read.csv(paste(lib_dir, "lib_element.csv", sep = "/"), sep = ",", header = T)
+lookup_element <- read[, 2:3]
+row.names(lookup_element) <- read[, 1]
+
+read <- read.csv(paste(lib_dir, "lib_modification.csv", sep = "/"), sep = ",", header = T)
+lookup_mod <- read[, 2:ncol(read)]
+row.names(lookup_mod) <- read[, 1]
+
+
+## ==== Main process ====
+
+#' XCMS
+if (opt$process) {
+
+  #' process multiple input files seperated by comma
+  #' wl-04-03-2019, Mon: add file directory option. Note that it is not for
+  #' galaxy.
+  if (dir.exists(opt$mzxml_file)) { ## file directory
+    opt$mzxml_file <- list.files(opt$mzxml_file,
+      pattern = "mzml|mzxml",
+      ignore.case = T, recursive = F,
+      full.names = TRUE
+    )
+  } else { ## multiple files
+    opt$mzxml_file <- str_vec(opt$mzxml_file)
+  }
+
+  #' handle sample names (especially for galaxy)
+  if (opt$samp_name == "") {
+    opt$samp_name <- opt$mzxml_file
+  } else {
+    opt$samp_name <- str_vec(opt$samp_name)
+  }
+  #' extract only sample names (use greedy match)
+  opt$samp_name <- gsub(".*/|\\..*$", "", opt$samp_name, perl = T)
+
+  #' Construct xcmsSet objects for peaks
+  xset <- xcmsSet(opt$mzxml_file, snames = opt$samp_name,
+    method = "matchedFilter", step = 0.1,
+    sigma = opt$FWHM / 2.3548, snthresh = opt$snthresh,
+    profmethod = opt$profmethod
+  )
+  #' wl-30-05-2019, Thu: findPeaks.matchedFilter is one of methods.
+
+  xset <- group(xset) #' slotNames(xset)
+
+  #' Corrects retention times
+  xset <- retcor(xset,
+    method = "obiwarp", profStep = 0.1,
+    plottype = "none"
+  ) # "deviation"
+  #' wl-15-03-2018, Thu: Possible memory problem?
+  #' wl-28-05-2019, Tue: 'profStep': step size (in m/z) to use for profile
+  #' generation. Smaller steps yield more precision at the cost of greater
+  #' memory usage. (from profStep-methods)
+  #' wl-30-05-2019, Thu: two methods: 'peakgroups' and 'obiwarp'
+
+  #' Group peaks from different samples together
+  xset <- group(xset, bw = 5, minfrac = opt$minfrac, mzwid = 0.025)
+  #' lwc-05-11-2013: three methods: group.density (default),
+  #'  group.mzClust and group.nearest.
+
+  #' Integrate areas of missing peaks
+  xset <- fillPeaks(xset)
+  #' Note: need mzML files to fill in missing peaks
+
+  #' Peak lists. (peak area: value = "into"; peak height: value = "maxo")
+  peaklist <- peakTable(xset,
+                        method = "maxint", value = "into",
+                        intensity = "maxo"
+                        ) #' peak area
+
+  #' round mz and rt, and kepp them
+  peaklist <- transform(peaklist, mz = round(mz, 4), rt = round(rt, 2))
+  peaklist <- peaklist[,c("mz","rt",opt$samp_name)]
+  #' wl-14-10-2019, Mon: directory will be random in planemo test. 
+  #' peaklist <- subset(peaklist, select = -c(mzmin, mzmax, rtmin, rtmax, npeaks))
+  #' peaklist <- peaklist[, -3] #' remove mzml directory name
+
+  if (opt$rdata) {
+    save(xset, peaklist, file = opt$rdata_out)
+  } 
+  
+} else {
+    load(opt$xset_file)
+}
+
+#' Deisotoping
+
+#' wl-28-05-2019, Tue: Use average of all samples.
+#' mz and intensity of the 1st sample
+#' spectra <- as.matrix(peaklist[, c(1, 3)])
+#' spectra <- cbind(spectra, "", "")
+#' colnames(spectra) <- c("mz.obs", "intensity", "isotope", "modification")
+
+tmp <- apply(peaklist[, -c(1, 2)], 1, mean)
+spectra <- as.matrix(cbind(
+  mz.obs = peaklist[, 1], intensity = tmp,
+  isotope = "", modification = ""
+))
+
+deisotoped <- deisotoping(
+  ppm = opt$ppm,
+  no_isotope = opt$no_isotope,
+  prop.1 = opt$prop_1,
+  prop.2 = opt$prop_2,
+  spectra = spectra
+)
+
+#' Annotating
+
+#' make library
+dbase <- makelibrary(
+  ionisation_mode = opt$ionisation_mode,
+  fixed = opt$fixed,
+  fixed_FA = opt$fixed_FA,
+  lookup_lipid_class = lookup_lipid_class,
+  lookup_FA = lookup_FA,
+  lookup_element = lookup_element
+)
+
+#' annotating
+annotated <- annotating(
+  ionisation_mode = opt$ionisation_mode,
+  deisotoped = deisotoped,
+  ppm.annotate = opt$ppm_annotate,
+  dbase = dbase
+)
+
+#' update and normalise peaklist
+indices <- match(deisotoped[, "mz.obs"], peaklist[, "mz"])
+tmp <- peaklist[indices, ]
+rownames(tmp) <- NULL
+final_peak <- cbind(annotated, tmp)
+
+
+#' normalising based on TIC
+tmp <- norm_tic(final_peak[, -c(1:3)], dim = 2)
+final_peak <- cbind(final_peak[, 1:3], tmp)
+
+#' save results
+write.table(final_peak, file = opt$peak_out, sep = "\t", row.names = F)
diff -r 000000000000 -r 55efed82d7ec lcms/lcms.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/lcms.xml	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,344 @@
+<!--
+    wl-28-05-2019, Tue: commence
+    wl-30-05-2019, Thu: XML works. use 'ln -sf' to override the existed one
+    wl-04-06-2019, Tue: help information and planemo test
+-->
+<tool id="lcms" name="lcms" version="0.1.0">
+  <description>
+    Processing, deisotyping and annotating of LC-MS data
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+
+  <!-- =============================================================== -->
+  <command detect_errors="exit_code">
+    <![CDATA[
+      #if $process.process_selector == "TRUE":
+        #for $file in $process.mzxml_file:
+          #if $file.is_of_type("mzxml")
+            ln -sf ${file} ${file}.mzXML &&
+          #else
+            ln -sf ${file} ${file}.mzML &&
+          #end if  
+        #end for
+      #end if
+
+      Rscript ${__tool_directory__}/lcms.R
+        --process '$process.process_selector'      
+        #if $process.process_selector == "TRUE":
+          --mzxml_file '$process.mzxml_file' 
+          --samp_name '${','.join([a.name for a in $process.mzxml_file])}'  
+          --FWHM '$process.FWHM'
+          --snthresh '$process.snthresh'
+          --profmethod '$process.profmethod'
+          --minfrac '$process.minfrac'
+          --rdata '$process.rdata'
+          #if $process.rdata:
+            --rdata_out '$rdata_out'
+          #end if
+        #else:
+          --xset_file '$process.xset_file' 
+        #end if
+
+        ## Making library
+        --ionisation_mode '$make_library.ionisation_mode'
+        --fixed '$make_library.fixed'
+        --fixed_FA '$make_library.fixed_FA'
+        
+        ## deisotope
+        --ppm '$deisotope.ppm'
+        --no_isotope '$deisotope.no_isotope'
+        --prop_1 '$deisotope.prop_1'
+        --prop_2 '$deisotope.prop_2'
+
+        ## annotate
+        --ppm_annotate '$annotate.ppm_annotate'
+
+        ## save annotated peak 
+        --peak_out '$peak_out'
+    ]]>
+  </command>
+
+  <!-- =============================================================== -->
+  <inputs>
+
+    <conditional name="process">
+      <param label="Process LC-MS data with mzML or mzXML format"
+             name="process_selector"
+             type="select"
+             help="Choose if you want to process MS data or only annotate it." >
+                <option value="TRUE" selected="True">perform processing</option>
+                <option value="FALSE">annotation of processed file</option>
+      </param>
+
+      <when value="TRUE">
+
+        <param name="mzxml_file" type="data"  format="mzxml,mzml" multiple="true" 
+              label="LC-MS data" optional="false"
+              help="At least two LC-MS data files (positive or negative mode) in mzXML 
+                    or mzML format." />
+
+          <!-- parameter for function xcmsSet. findPeaks.matchedFilter is used. -->
+          <param name="FWHM" type="float" value="3"
+                label="FWHM of matched filtration gaussian model peak."
+                help = "(FWHM) Approximate FWHM (in seconds) of chromatographic peaks." />
+
+          <param name="snthresh" type="float" value="5"
+                label="The signal to noise threshold"
+                help = "(snthresh) Defining the signal to noise cutoff to be used in 
+                        the chromatographic peak detection step" />
+
+          <param name="profmethod" type="select"
+             label="Select a method for profile generation"
+             help="(profmethod) Method to use for profile generation.">
+             <option value="binlin" selected="true">binlin</option>
+             <option value="bin">bin</option>
+             <option value="binlinbase">binlinbase</option>
+             <option value="intlin">intlin</option>
+          </param>
+
+          <!-- parameter for function group. group.density (default) is used. -->
+          <param name="minfrac" type="float" value="0.25"
+                label="Minimum fraction"
+                help = "(minfrac) Minimum fraction of samples necessary for it to be a
+                        valid peak group" />
+
+          <param name="rdata" type="boolean" 
+                  truevalue="TRUE" falsevalue="FALSE" checked="true" 
+                  label="Save xcms results?"
+                  help="Save xcmsSet R file after runninbg xcms."/>
+
+       </when>
+
+      <when value="FALSE">
+        <param name="xset_file" format="rdata" type="data"
+               label="xcmsSet R data"
+               help="xcmsSet R data file produced by xcms" />
+      </when>
+      
+    </conditional>
+
+    <section name="make_library" title="Making library" > 
+
+      <param name="ionisation_mode" type="select"
+              label="Specify ionisation mode"
+              help="Choose 'positive' or 'negative', will determine
+                    which lipid classes are in database"
+              display="radio">
+            <option value="positive" selected="true">positive</option>
+            <option value="negative">negative</option>
+      </param>
+
+      <param name="fixed" type="boolean" 
+              truevalue="TRUE" falsevalue="FALSE" 
+              checked="false" label="SN position fixed or not"
+              help="Defines if one of the SN positions is fixed, default
+                    is false." />
+
+      <param name="fixed_FA" type="float" value="16"
+              label="Fixed FA"
+              help="Defines the name of the fixed FA eg 16, 18.1, 20.4." />
+    </section>
+
+    <section name="deisotope"
+              title="Perform deisotoping on LC-MS data">
+      
+      <param name="ppm" type="integer" value="5" label="Tolerance (ppm)"
+              help="Tolerance (ppm) within which mass of isotope must
+                    be within"/>
+
+      <param name="no_isotope" type="integer" value="2"
+              min="1" max="2"
+              label="Number of isotopes"
+              help="Number of isotopes to consider (1 or 2)"/>
+
+      <param name="prop_1" type="float" value="0.9" min="0" max="1"
+              label="First Proportion"
+              help="Proportion of monoisotope intensity the 1st isotope
+                    intensity must not exceed"/>
+
+      <param name="prop_2" type="float" value="0.5" min="0" max="1"
+              label="Second proportion"
+              help="Proportion of monoisotope intensity the 2nd isotope
+                    intensity must not exceed"/>
+    </section>
+
+    <section name="annotate"
+              title="Perform putative annotation on deisotoped LC-MS data">
+      <param name="ppm_annotate" type="integer" value="15"
+              label="Specify ppm threshold for annotation"
+              help="Defines ppm threshold for which |observed m/z -
+                    theoretical m/z| must be less than for annotation to be
+                    retained. Suggest to use same mass tolerance 
+                    as bin width." /> 
+    </section>
+    
+  </inputs>
+
+  <!-- =============================================================== -->
+  <outputs>
+    <data format="tabular" name="peak_out"
+          label="Annotated peak table on ${on_string}">
+    </data>
+    
+    <data format="rdata" name="rdata_out"
+          label="xcmsSet R results on ${on_string}">
+          <filter> 
+            ((
+            process['process_selector'] == "TRUE" and
+            process['rdata'] == True
+            ))
+          </filter>
+    </data>
+
+  </outputs>
+
+  <!-- =============================================================== -->
+  <tests>
+    <test>
+      <param name="process_selector" value="TRUE" /> 
+      <param name="mzxml_file" value="lcms_pos/ZH_190918_mann_liver_pos_001.mzML,lcms_pos/ZH_190918_mann_liver_pos_002.mzML" />
+      <param name="ionisation_mode" value="positive" /> 
+      <param name="FWHM" value="3" /> 
+      <param name="snthresh" value="5" /> 
+      <param name="profmethod" value="binlin" />
+      <param name="minfrac" value="0.25" /> 
+      <param name="rdata" value="TRUE" /> 
+      <output name="peak_out" file="res/peak_pos.tsv" />
+      <output name="rdata_out" file="res/xset_pos.rdata" compare="sim_size" delta="1000" />
+    </test>
+
+    <test>
+      <param name="process_selector" value="TRUE" /> 
+      <param name="mzxml_file" value="lcms_neg/ZH_180918_mann_neg_001.mzML,lcms_neg/ZH_180918_mann_neg_002.mzML" />
+      <param name="ionisation_mode" value="negative" /> 
+      <param name="FWHM" value="3" /> 
+      <param name="snthresh" value="5" /> 
+      <param name="profmethod" value="binlin" />
+      <param name="minfrac" value="0.25" /> 
+      <param name="rdata" value="TRUE" /> 
+      <output name="peak_out" file="res/peak_neg.tsv" />
+      <output name="rdata_out" file="res/xset_neg.rdata" compare="sim_size" delta="1000" />
+    </test>
+
+    <test>
+      <param name="process_selector" value="FALSE" /> 
+      <param name="xset_file" value="res/xset_pos.rdata" /> 
+      <param name="ionisation_mode" value="positive" /> 
+      <param name="fixed" value="FALSE" /> 
+      <param name="fixed_FA" value="16" /> 
+      <param name="ppm" value="5" /> 
+      <param name="ppm_annotate" value="15" /> 
+      <output name="peak_out" file="res/peak_pos.tsv" />
+    </test>
+
+    <test>
+      <param name="process_selector" value="FALSE" /> 
+      <param name="xset_file" value="res/xset_neg.rdata" /> 
+      <param name="ionisation_mode" value="negative" /> 
+      <param name="fixed" value="FALSE" /> 
+      <param name="fixed_FA" value="16" /> 
+      <param name="ppm" value="5" /> 
+      <param name="ppm_annotate" value="15" /> 
+      <output name="peak_out" file="res/peak_neg.tsv" />
+    </test>
+  </tests>
+
+  <!-- =============================================================== -->
+  <help>
+
+LC-MS processing, deisotoping and annotating
+============================================
+
+
+Description
+-----------
+
+This tool performs deisotyping and annotating of LC-MS data. 
+
+Inputs
+------
+
+There are two input data formats, either ``mzML/mzXML`` or R data file for
+deisotyping and annotating analysis. 
+
+**\1. LC-MS data with mzML/mzXML format**
+
+The LC-MS data format is ``mzML`` or ``mzXML`` which can be converted from
+raw data by ``MSConvert`` of ProteoWizard_. Each file represents one sample
+or replicate. Select multiple ``mzXML`` files for processing. The input data
+will be either positive or negative mode. They cannot be mixed up.
+
+These ``mzML/mzXML`` files are converted by R package ``xcms`` into R data
+files. The algorithm for peak detection is fixed as ``matchedFilter`` and
+retention times alignment across samples with ``obiwarp`` method. The
+``density`` method is employed for the peak grouping. The parameters for
+user to choose are:
+
+- ``FWHM``: specifying the full width at half maximum of matched filtration
+  Gaussian model peak. Default value is 3.
+- ``snthresh``: defining the signal to noise cutoff to be used in the
+  chromatographic peak detection step. Default value is 5.
+- ``profmethod``: Method to use for profile generation. Supported values are
+  "bin", "binlin" (default), "binlinbase" and "intlin". "bin" is better for centroid data, "binlin" for profile data.
+- ``minfrac``: minimum fraction (fefault: 0.25) of samples necessary in at
+  least one of the sample groups for it to be a valid group.,
+   
+**\2. R data file**
+
+Already processed data can be loaded as ``xcmsSet`` object R data file, produced by the R package ``xcms``.
+
+.. _ProteoWizard: http://proteowizard.sourceforge.net/
+
+
+Parameters
+----------
+
+See brief description on the setting of parameters for deisotyping and
+annotating above.
+
+Outputs
+----------
+
+Annotated Peak Table
+~~~~~~~~~~~~~~~~~~~~
+
+The peak area is normalised by TIC and the annotated peak table is in
+tabular format:
+
+=================================== ========  ======= =========== =========== =========== 
+annotated                           mz        rt      pos_001     pos_002     pos_003
+=================================== ========  ======= =========== =========== =========== 
+[Cer(42:2)+H]                       648.6199  386.44  509476.1705 90147.43029 17059.58466
+[DG-H20(38:3)+Na][DG-H20(40:6)+H]   651.5342  389.92  89868.92836 76789.83982 40555.16262
+[Cer(40:5)+K]                       652.5009  56.93   1967715.965 1904828.953 132351.8552
+[DG-H20(40:5)+H]                    653.5499  396.17  88798.76816 68192.75595 10524.34529
+=================================== ========  ======= =========== =========== =========== 
+
+      |
+
+xcmsSet R data file (OPTIONAL)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+``xcmsSet`` R results are saved as an R file ``rdata`` for advanced users to perform further analysis.
+
+
+  </help>
+  
+  <citations>
+    <citation type="bibtex">
+    @misc{, 
+      title = {LC-MS Processing}, 
+      url = {https://github.com/hallz/lcms_processing_}, 
+      journal = {GitHub}, 
+      author = {hallz}, 
+      year = {2016}, 
+      month={Feb}}
+    }
+    </citation>
+  </citations>
+
+</tool>
diff -r 000000000000 -r 55efed82d7ec lcms/lcms_func.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/lcms_func.R	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,510 @@
+
+#' ========================================================================
+#' wl-21-05-2019, Tue: take this function from 'massPix' and remove 
+#'  'sel.class' argument
+makelibrary <- function(ionisation_mode = c("positive","negative"), 
+                        fixed = F, fixed_FA, lookup_lipid_class, 
+                        lookup_FA, lookup_element) {
+  cat("\nMaking library of lipid masses...\n")
+  ionisation_mode <- match.arg(ionisation_mode)
+  if (ionisation_mode == "positive") {
+    sel.class <- c(
+      T, # TG
+      T, # DG
+      T, # PC
+      F, # PA
+      T, # PE
+      T, # PS
+      F, # PG
+      F, # PI
+      F, # PIP
+      F, # PIP2
+      F, # PIP3
+      T, # LysoPC
+      T, # DG-H20
+      T, # CE
+      F, # FFA
+      T, # SM
+      T # Cer
+    )
+  }
+
+  if (ionisation_mode == "negative") {
+    sel.class <- c(
+      F, # TG
+      F, # DG
+      T, # PC
+      T, # PA
+      T, # PE
+      T, # PS
+      T, # PG
+      T, # PI
+      T, # PIP
+      T, # PIP2
+      T, # PIP3
+      F, # LysoPC
+      F, # DG-H20
+      F, # CE
+      T, # FFA
+      F, # SM
+      T # Cer - ZLH changed this to true 20.03.18
+    )
+  }
+
+  lookup_lipid_class <- cbind(lookup_lipid_class, sel.class)
+
+  #' FAs to use in library
+  FA_expt <- list(
+    "10", "12", "14", "15", "16", "16.1", "17", "17.1", "18", "18.1",
+    "18.2", "18.3", "20.3", "20.4", "20.5", "21", "22", "22.5",
+    "22.6", "23", "24.1"
+  )
+
+  library <- numeric()
+  for (i in 1:nrow(lookup_lipid_class)) {
+    if (lookup_lipid_class[i, "sel.class"] == T) {
+      #' key variables
+      rounder <- 3 # number of decimals the rounded masses are rounded to.
+      #' lipidclass = "TG"
+      lipidclass <- row.names(lookup_lipid_class[i, ])
+
+      #' determine how many FAs places to be used for combination and
+      #' generate combination of FAs
+      FA_number <- as.numeric(lookup_lipid_class[lipidclass, "FA_number"])
+      if (fixed == TRUE) FAnum <- FA_number - 1 else FAnum <- FA_number
+      s1 <- combn(FA_expt, FAnum)
+
+      #' if one place is fixed add this FA to the matrix
+      if (fixed == TRUE) {
+        s1 <- rbind(s1, "fixed" = fixed_FA)
+        FAnum <- FAnum + 1
+      }
+
+      #' if sn2 or sn3 does not have FA bind 'empty' FA channel.
+      if (FAnum == 1) {
+        s1 <- rbind(s1, sn2 <- vector(mode = "numeric", length = ncol(s1)), sn3 <- vector(mode = "numeric", length = ncol(s1)))
+        FAnum <- FAnum + 2
+      }
+      if (FAnum == 2) {
+        s1 <- rbind(s1, sn3 <- vector(mode = "numeric", length = ncol(s1)))
+        FAnum <- FAnum + 1
+      }
+
+
+      #' label the matrix
+      if (FAnum == 3) row.names(s1) <- c("FA1", "FA2", "FA3")
+
+      #' add rows to matrix for massofFAs and formula
+      massofFAs <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, massofFAs)
+      formula <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, formula)
+      #' row.names(s1) <-c("FA1", "FA2","FA3", "massofFAs")
+      for (i in 1:ncol(s1)) {
+
+        #' for 3 FAs
+        if (FAnum == 3) {
+          FA_1 <- as.character((s1[1, i]))
+          FA_2 <- as.character((s1[2, i]))
+          FA_3 <- as.character((s1[3, i]))
+          s1["massofFAs", i] <- as.numeric((lookup_FA[FA_1, "FAmass"])) + as.numeric((lookup_FA[FA_2, "FAmass"])) + as.numeric((lookup_FA[FA_3, "FAmass"]))
+          #' determine the formula
+          temp_carbon <- as.numeric((lookup_FA[FA_1, "FAcarbon"])) + as.numeric((lookup_FA[FA_2, "FAcarbon"])) + as.numeric((lookup_FA[FA_3, "FAcarbon"]))
+          temp_doublebond <- as.numeric((lookup_FA[FA_1, "FAdoublebond"])) + as.numeric((lookup_FA[FA_2, "FAdoublebond"])) + as.numeric((lookup_FA[FA_3, "FAdoublebond"]))
+          s1["formula", i] <- paste(lipidclass, "(", temp_carbon, ":", temp_doublebond, ")", sep = "")
+        }
+      }
+
+      #' calculate total mass
+      totalmass <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, totalmass)
+
+      for (i in 1:ncol(s1)) {
+        s1["totalmass", i] <- as.numeric(s1["massofFAs", i]) + as.numeric(as.character(lookup_lipid_class[lipidclass, "headgroup_mass"])) - (as.numeric(lookup_lipid_class[lipidclass, "FA_number"]) * as.numeric(lookup_element["H", "mass"]))
+      }
+
+      #' make rows for charged lipids masses
+      protonated <- vector(mode = "numeric", length = ncol(s1))
+      ammoniated <- vector(mode = "numeric", length = ncol(s1))
+      sodiated <- vector(mode = "numeric", length = ncol(s1))
+      potassiated <- vector(mode = "numeric", length = ncol(s1))
+      deprotonated <- vector(mode = "numeric", length = ncol(s1))
+      chlorinated <- vector(mode = "numeric", length = ncol(s1))
+      acetate <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, protonated, ammoniated, sodiated, potassiated, deprotonated, chlorinated, acetate)
+
+      #' calculate charged lipids masses
+      for (i in 1:ncol(s1)) {
+        s1["protonated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["H", "mass"])), digits = 4)
+        s1["ammoniated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["NH4", "mass"])), digits = 4)
+        s1["sodiated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["Na", "mass"])), digits = 4)
+        s1["potassiated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["K", "mass"])), digits = 4)
+        s1["deprotonated", i] <- round((as.numeric(s1["totalmass", i]) - as.numeric(lookup_element["H", "mass"])), digits = 4)
+        s1["chlorinated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["Cl", "mass"])), digits = 4)
+        s1["acetate", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["CH3COO", "mass"])), digits = 4)
+      }
+
+      #' make rows for rounded charged lipids masses
+      round.protonated <- vector(mode = "numeric", length = ncol(s1))
+      round.ammoniated <- vector(mode = "numeric", length = ncol(s1))
+      round.sodiated <- vector(mode = "numeric", length = ncol(s1))
+      round.potassiated <- vector(mode = "numeric", length = ncol(s1))
+      round.deprotonated <- vector(mode = "numeric", length = ncol(s1))
+      round.chlorinated <- vector(mode = "numeric", length = ncol(s1))
+      round.acetate <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, round.protonated, round.ammoniated, round.sodiated, round.potassiated, round.deprotonated, round.chlorinated, round.acetate)
+
+      #' calculate rounded charged lipids masses
+      for (i in 1:ncol(s1)) {
+        s1["round.protonated", i] <- round(as.numeric(s1["protonated", i]), digits = rounder)
+        s1["round.ammoniated", i] <- round(as.numeric(s1["ammoniated", i]), digits = rounder)
+        s1["round.sodiated", i] <- round(as.numeric(s1["sodiated", i]), digits = rounder)
+        s1["round.potassiated", i] <- round(as.numeric(s1["potassiated", i]), digits = rounder)
+        s1["round.deprotonated", i] <- round(as.numeric(s1["deprotonated", i]), digits = rounder)
+        s1["round.chlorinated", i] <- round(as.numeric(s1["chlorinated", i]), digits = rounder)
+        s1["round.acetate", i] <- round(as.numeric(s1["acetate", i]), digits = rounder)
+      }
+
+      library <- cbind(library, s1)
+    }
+  }
+  return(library)
+}
+
+#' ========================================================================
+#' wl-23-03-2018, Fri: debug and tidy up
+#' wl-21-05-2019, Tue: different from massPix
+deisotoping <- function(ppm = 5, no_isotopes = 2, prop.1 = 0.9, prop.2 = 0.5,
+                        spectra = spectra) {
+  C13_1 <- 1.003355
+  C13_2 <- C13_1 * 2
+  k <- 0
+  m <- 0
+
+  #' run loop to find isotopes for each ion.
+  for (i in (1:(nrow(spectra) - 1))) {
+    #' values of search
+    mass <- as.numeric(spectra[i, 1])
+    intensity <- as.numeric(spectra[i, 2])
+    #' calculated values
+    offset <- (ppm * mass) / 1000000
+
+    #' find isotope with ppm filter on isotpe
+    search <- round((mass + C13_1), digits = 3)
+    top <- search + offset
+    bottom <- search - offset
+    result <- spectra[as.numeric(spectra[, "intensity"]) <= (intensity * prop.1) & spectra[, 1] >= bottom & spectra[, 1] <= top & spectra[, "isotope"] == "", ]
+    result <- rbind(result, blank1 = "", blank2 = "")
+
+    if (no_isotopes == 2) {
+      #' find isotope with ppm filter on isotpe
+      search <- round((mass + C13_2), digits = 3)
+      top <- search + offset
+      bottom <- search - offset
+      result_2 <- spectra[as.numeric(spectra[, "intensity"]) <= (intensity * prop.2) & spectra[, 1] >= bottom & spectra[, 1] <= top & spectra[, "isotope"] == "", ]
+      result_2 <- rbind(result_2, blank1 = "", blank2 = "")
+    }
+
+    if (nrow(result) > 2) {
+      k <- k + 1
+      spectra[i, "isotope"] <- paste(spectra[i, "isotope"], " ", "[", k, "]", "[M]", sep = "")
+      for (j in 1:(nrow(result) - 2)) {
+        indices <- which(spectra == result[j, 1], arr.ind = TRUE)
+        spectra[indices[, "row"], "isotope"] <- paste(spectra[indices[, "row"], "isotope"], " ", "[", k, "]", "[M+1]", sep = "")
+      }
+      if (no_isotopes == 2 && nrow(result_2) > 2) {
+        for (j in 1:(nrow(result_2) - 2)) {
+          indices <- which(spectra == result_2[j, 1], arr.ind = TRUE)
+          spectra[indices[, "row"], "isotope"] <- paste(spectra[indices[, "row"], "isotope"], " ", "[", k, "]", "[M+2]", sep = "")
+        }
+      }
+    }
+  }
+
+  allpeaks   <- as.data.frame(spectra)
+  deisotoped <- allpeaks[(grep("\\[M\\+", allpeaks$isotope, invert = T)), ]
+  isotopes   <- allpeaks[(grep("\\[M\\+", allpeaks$isotope, invert = F)), ]
+
+  summary <- paste(length(as.vector(deisotoped$mz.obs)),
+    "monoisotopic peaks retained and",
+    length(as.vector(isotopes$mz.obs)),
+    "C13 isotopes discarded from",
+    length(as.vector(allpeaks$mz.obs)),
+    "detected ions",
+    sep = " "
+  )
+  print(summary)
+
+  #' results <- list(allpeaks = allpeaks, deisotoped = deisotoped, isotopes = isotopes)
+  #' return(results)
+
+  return(deisotoped)
+}
+
+#' ========================================================================
+#' wl-23-03-2018, Fri: Debug and tidy up.
+#' wl-21-05-2019, Tue: almost same as massPix
+#' wl-23-05-2019, Thu: Fix some bugs
+annotating <- function(ionisation_mode, deisotoped,
+                       #' adducts = c(H = T, NH4 = F, Na = T, K = F, dH = F, Cl = F, OAc = F),
+                       ppm.annotate = 10, dbase) {
+  cat("Starting annotation\n")
+
+  d.finalmz   <- as.vector(deisotoped$mz.obs)
+  s1          <- dbase
+  spectra     <- cbind(round(as.numeric(d.finalmz), digits = 3), d.finalmz)
+  combined    <- vector()
+  sel.adducts <- vector()
+  index       <- 13 # offset to search only rounded masses in library
+
+  if (ionisation_mode == "positive") {
+    adducts <- c(H = T, NH4 = F, Na = T, K = T, dH = F, Cl = F, OAc = F)
+  }
+  if (ionisation_mode == "negative") {
+    adducts <- c(H = F, NH4 = F, Na = F, K = F, dH = T, Cl = T, OAc = F)
+  }
+  for (a in 1:length(adducts)) {
+    if (adducts[a] == T) sel.adducts <- c(sel.adducts, index + a)
+  }
+
+  for (i in 1:nrow(spectra)) {
+    search <- as.numeric(spectra[i, 1])
+    offset <- (ppm.annotate * search) / 1000000
+    top <- search + offset
+    bottom <- search - offset
+    result <- which(s1[sel.adducts, ] >= bottom & s1[sel.adducts, ] <= top, 
+                    arr.ind = TRUE)
+
+    #' =========================
+    #' wl-23-05-2019, Thu: famous R problem: 
+    #' Error in if (condition)  : argument is of length zero
+    #' =========================
+    #' if (nrow(result) > 0) {  
+    if (length(result) > 0) {
+      for (j in 1:nrow(result)) {
+        col <- result[j, "col"]
+        row <- result[j, "row"]
+        row <- sel.adducts[row]
+
+        #' determine the adduct that was matched, summarising match 
+        #' information from library for matched mass (as 'data')
+        #' determine which adduct
+        if (row == "14") {
+          adduct <- "protonated"
+          name.adduct <- "H"
+        }
+        if (row == "15") {
+          adduct <- "ammoniated"
+          name.adduct <- "NH4"
+        }
+        if (row == "16") {
+          adduct <- "sodiated"
+          name.adduct <- "Na"
+        }
+        if (row == "17") {
+          adduct <- "potassiated"
+          name.adduct <- "K"
+        }
+        if (row == "18") {
+          adduct <- "deprotonated"
+          name.adduct <- "-H"
+        }
+        if (row == "19") {
+          adduct <- "chlorinated"
+          name.adduct <- "Cl"
+        }
+        if (row == "20") {
+          adduct <- "acetate"
+          name.adduct <- "OAc"
+        }
+
+        a.ppm <- round(abs(((as.numeric(spectra[i, 2]) - as.numeric(s1[adduct, col])) / as.numeric(spectra[i, 2])) * 1000000), digits = 1)
+
+        #' make vector with summary of match and paired match
+        data <- c(
+          s1[row, col], s1[adduct, col], spectra[i, 2], a.ppm,
+          s1["formula", col], name.adduct, s1["protonated", col],
+          s1["FA1", col], s1["FA2", col], s1["FA3", col]
+        )
+
+        #' make matrix of search results
+        combined <- rbind(combined, unlist(data, use.names = F))
+      }
+    }
+
+  }
+
+  if (length(combined) > 0) {
+    colnames(combined) <- c(
+      "mz.matched", "mz.matched.lib", "mz.observed",
+      "ppm", "formula", "adduct", "mz.lib.protonated",
+      "FA1", "FA2", "FA3"
+    )
+
+    ids <- unique.matrix(combined[, c(3, 5, 6)])
+    annotations <- cbind(d.finalmz, "")
+
+    for (i in 1:nrow(annotations)) {
+      result <- which(ids[, 1] == annotations[i, 1], arr.ind = T)
+      if (length(result) > 0) {
+        for (j in 1:length(result)) {
+          annotations[i, 2] <- paste(annotations[i, 2], "[",
+            ids[result[j], "formula"], "+",
+            ids[result[j], "adduct"], "]",
+            sep = ""
+          )
+        }
+      }
+    }
+
+    summary <- paste(length(annotations[annotations[, 2] != "", 2]), "from",
+      length(as.vector(deisotoped$mz.obs)),
+      "monoisotopic peaks were annoated (using accuract mass) with a",
+      ppm.annotate, "ppm tollerance",
+      sep = " "
+    )
+    print(summary)
+
+    return(annotations[, 2])
+  } else { #' wl-23-05-2019, Thu: should give exit code.
+    print("No annotations were made")
+  }
+
+}
+
+#' ========================================================================
+#' wl-28-05-2019, Tue: normalisation based on TIC
+#'   x - numeric data matrix
+#'   dim - normalisation based on row (1) or column (2)
+norm_tic <- function(x, dim = 1) {
+  scale <- apply(x, dim, function(x) sum(x, na.rm = T))
+  scale <- scale/mean(scale, na.rm = T)
+  x <- sweep(x, dim, scale, "/")
+}
+
+## ==== DEBUG: get peaklist using 'goupval' from 'xcms' ====
+
+if (F){
+  #' peakmat <- xcms::peaks(xset)
+  #' Note: two arguments in 'groupval', 'value' and 'intensity' will use this
+  #' matrix's intensity columns
+
+  grpmat <- groups(xset) #' object@groups  #' dim(grpmat)
+  #' values <- groupval(xset, method="medret", value="into")
+  if (T){  #' peak area
+    values <- groupval(xset, method = "maxint", value = "into", intensity = "maxo")
+  } else { #' peak height
+    values <- groupval(xset, method = "maxint", value = "maxo", intensity = "maxo")
+  }
+  #' wl-20-03-2018, Tue: it seems that only 'value' to decide the intensity to
+  #' be returned. For details, see source code of 'groupval'
+
+  peaklist <- data.frame(cbind(grpmat, values), row.names = NULL)
+  colnames(peaklist) <- gsub("mzmed", "mz", colnames(peaklist))
+  colnames(peaklist) <- gsub("rtmed", "rt", colnames(peaklist))
+} 
+
+## ==== DEBUG: peakTable from 'xcms' ====
+
+if (F) {
+  #' ------------------------------------------------------------------
+  #' wl-20-03-2018, Tue: Use 'peakTable' directly.
+  peaklist  <- peakTable(xset, method="maxint", value="into", intensity="maxo")
+
+  #' =====================================================================
+  #' wl-20-03-2018, Tue: Note that the dot arguments sgould be 'groupval'
+  setMethod("peakTable", "xcmsSet", function(object, filebase = character(), ...) {
+    if (length(sampnames(object)) == 1) {
+      return(object@peaks)
+    }
+
+    if (nrow(object@groups) < 1) {
+      stop("First argument must be an xcmsSet with group information or contain only one sample.")
+    }
+
+    groupmat <- groups(object)
+
+
+    if (!"value" %in% names(list(...))) {
+      ts <- data.frame(cbind(groupmat, groupval(object, value = "into", ...)), row.names = NULL)
+    } else {
+      ts <- data.frame(cbind(groupmat, groupval(object, ...)), row.names = NULL)
+    }
+
+    cnames <- colnames(ts)
+
+    if (cnames[1] == "mzmed") {
+      cnames[1] <- "mz"
+    } else {
+      stop("mzmed column missing")
+    }
+    if (cnames[4] == "rtmed") {
+      cnames[4] <- "rt"
+    } else {
+      stop("mzmed column missing")
+    }
+
+    colnames(ts) <- cnames
+
+    if (length(filebase)) {
+      write.table(ts, paste(filebase, ".tsv", sep = ""),
+        quote = FALSE,
+        sep = "\t", col.names = NA
+      )
+    }
+
+    ts
+  })
+}
+
+## ==== DEBUG: getPeaklist from 'CAMERA' ====
+
+if (F) {
+  #' ------------------------------------------------------------------
+  #' wl-15-05-2019, Wed: get peak list after annotation by CAMERA.
+  #' Note: need the original mzML files
+  library(CAMERA)
+  xsa         <- annotate(xset, cor_eic_th=0)
+  peaklist.1  <- getPeaklist(xsa)
+  #' or get peak list directly from CAMERA's hidden function
+  peaklist.2 <- CAMERA:::getPeaks_selection(xset)
+
+  #' =====================================================================
+  #' Create complete feature table from CAMERA
+  #' xs     - xcmsSet object
+  #' method - groupval parameter method
+  #' value  - groupval parameter method
+  getPeaks_selection <- function(xs, method = "medret", value = "into") {
+    if (!class(xs) == "xcmsSet") {
+      stop("Parameter xs is no xcmsSet object\n")
+    }
+
+    #' Testing if xcmsSet is grouped
+    if (nrow(xs@groups) > 0 && length(xs@filepaths) > 1) {
+      #' get grouping information
+      groupmat <- groups(xs)
+      #' generate data.frame for peaktable
+      ts <- data.frame(cbind(groupmat, groupval(xs, method = method, value = value)), row.names = NULL)
+      ## rename column names
+      cnames <- colnames(ts)
+      if (cnames[1] == "mzmed") {
+        cnames[1] <- "mz"
+      } else {
+        stop("Peak information ?!?")
+      }
+      if (cnames[4] == "rtmed") {
+        cnames[4] <- "rt"
+      } else {
+        stop("Peak information ?!?")
+      }
+      colnames(ts) <- cnames
+    } else if (length(sampnames(xs)) == 1) { # Contains only one sample?
+      ts <- xs@peaks
+    } else {
+      stop("First argument must be a xcmsSet with group information or contain only one sample.")
+    }
+
+    return(as.matrix(ts))
+  }
+
+}
diff -r 000000000000 -r 55efed82d7ec lcms/lcms_ori.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/lcms_ori.R	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,540 @@
+#' Script to process lcms data using xcms
+#' Functions for making lipid library, deisotoping and annotating were from
+#' Image Scope (Nick Bond) and modified for use with lcms data
+#' Z.Hall, Oct 2014
+#' -----------------------------------------------------------------------
+#' wl-12-03-2018, Mon: commence
+#' wl-15-03-2018, Thu: tidy R codes
+#' wl-20-05-2019, Mon: Some notes:
+#'  - Use peak area instead of peak height for deisotyping
+#'  - Deisotyping based on peaks with/without missing value filling. Should
+#'    based on MV filling
+#'  - Deisotyping based on mz and the first sample's intensity. Should use
+#'    average of all sample intesity
+#'  - should use 'peakTable' instead of 'low level' function such as
+#'    'groupval' and 'groupnames'. If so, R package 'reshape2' funcion
+#'    'colsplit' is no longer needed.
+
+library(xcms)
+library(reshape2)
+
+## ==== Functions ====
+#' Make lipid library
+makelibrary <- function(sel.class, fixed = F, fixed_FA, lookup_lipid_class,
+                        lookup_FA, lookup_element) {
+  print("Making library of lipid masses...")
+  lookup_lipid_class <- cbind(lookup_lipid_class, sel.class)
+
+  library <- numeric()
+  for (i in 1:nrow(lookup_lipid_class)) {
+    if (lookup_lipid_class[i, "sel.class"] == T) {
+      #' key variables
+      rounder <- 3 # number of decimals the rounded masses are rounded to.
+      #' lipidclass = "TG"
+      lipidclass <- row.names(lookup_lipid_class[i, ])
+
+      #' determine how many FAs places to be used for combination and generate combination of FAs
+      FA_number <- as.numeric(lookup_lipid_class[lipidclass, "FA_number"])
+      if (fixed == TRUE) FAnum <- FA_number - 1 else FAnum <- FA_number
+      s1 <- combn(FA_expt, FAnum)
+
+      #' if one place is fixed add this FA to the matrix
+      if (fixed == TRUE) {
+        s1 <- rbind(s1, "fixed" = fixed_FA)
+        FAnum <- FAnum + 1
+      }
+
+      #' if sn2 or sn3 does not have FA bind 'empty' FA channel.
+      if (FAnum == 1) {
+        s1 <- rbind(s1, sn2 <- vector(mode = "numeric", length = ncol(s1)), sn3 <- vector(mode = "numeric", length = ncol(s1)))
+        FAnum <- FAnum + 2
+      }
+      if (FAnum == 2) {
+        s1 <- rbind(s1, sn3 <- vector(mode = "numeric", length = ncol(s1)))
+        FAnum <- FAnum + 1
+      }
+
+
+      #' label the matrix
+      if (FAnum == 3) row.names(s1) <- c("FA1", "FA2", "FA3")
+
+      #' add rows to matrix for massofFAs and formula
+      massofFAs <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, massofFAs)
+      formula <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, formula)
+      #' row.names(s1) <-c("FA1", "FA2","FA3", "massofFAs")
+      for (i in 1:ncol(s1)) {
+
+        #' for 3 FAs
+        if (FAnum == 3) {
+          FA_1 <- as.character((s1[1, i]))
+          FA_2 <- as.character((s1[2, i]))
+          FA_3 <- as.character((s1[3, i]))
+          s1["massofFAs", i] <- as.numeric((lookup_FA[FA_1, "FAmass"])) + as.numeric((lookup_FA[FA_2, "FAmass"])) + as.numeric((lookup_FA[FA_3, "FAmass"]))
+          #' determine the formula
+          temp_carbon <- as.numeric((lookup_FA[FA_1, "FAcarbon"])) + as.numeric((lookup_FA[FA_2, "FAcarbon"])) + as.numeric((lookup_FA[FA_3, "FAcarbon"]))
+          temp_doublebond <- as.numeric((lookup_FA[FA_1, "FAdoublebond"])) + as.numeric((lookup_FA[FA_2, "FAdoublebond"])) + as.numeric((lookup_FA[FA_3, "FAdoublebond"]))
+          s1["formula", i] <- paste(lipidclass, "(", temp_carbon, ":", temp_doublebond, ")", sep = "")
+        }
+      }
+
+      #' calculate total mass
+      totalmass <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, totalmass)
+
+      for (i in 1:ncol(s1)) {
+        s1["totalmass", i] <- as.numeric(s1["massofFAs", i]) + as.numeric(as.character(lookup_lipid_class[lipidclass, "headgroup_mass"])) - (as.numeric(lookup_lipid_class[lipidclass, "FA_number"]) * as.numeric(lookup_element["H", "mass"]))
+      }
+
+      #' make rows for charged lipids masses
+      protonated <- vector(mode = "numeric", length = ncol(s1))
+      ammoniated <- vector(mode = "numeric", length = ncol(s1))
+      sodiated <- vector(mode = "numeric", length = ncol(s1))
+      potassiated <- vector(mode = "numeric", length = ncol(s1))
+      deprotonated <- vector(mode = "numeric", length = ncol(s1))
+      chlorinated <- vector(mode = "numeric", length = ncol(s1))
+      acetate <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, protonated, ammoniated, sodiated, potassiated, deprotonated, chlorinated, acetate)
+
+      #' calculate charged lipids masses
+      for (i in 1:ncol(s1)) {
+        s1["protonated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["H", "mass"])), digits = 4)
+        s1["ammoniated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["NH4", "mass"])), digits = 4)
+        s1["sodiated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["Na", "mass"])), digits = 4)
+        s1["potassiated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["K", "mass"])), digits = 4)
+        s1["deprotonated", i] <- round((as.numeric(s1["totalmass", i]) - as.numeric(lookup_element["H", "mass"])), digits = 4)
+        s1["chlorinated", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["Cl", "mass"])), digits = 4)
+        s1["acetate", i] <- round((as.numeric(s1["totalmass", i]) + as.numeric(lookup_element["CH3COO", "mass"])), digits = 4)
+      }
+
+      #' make rows for rounded charged lipids masses
+      round.protonated <- vector(mode = "numeric", length = ncol(s1))
+      round.ammoniated <- vector(mode = "numeric", length = ncol(s1))
+      round.sodiated <- vector(mode = "numeric", length = ncol(s1))
+      round.potassiated <- vector(mode = "numeric", length = ncol(s1))
+      round.deprotonated <- vector(mode = "numeric", length = ncol(s1))
+      round.chlorinated <- vector(mode = "numeric", length = ncol(s1))
+      round.acetate <- vector(mode = "numeric", length = ncol(s1))
+      s1 <- rbind(s1, round.protonated, round.ammoniated, round.sodiated, round.potassiated, round.deprotonated, round.chlorinated, round.acetate)
+
+      #' calculate rounded charged lipids masses
+      for (i in 1:ncol(s1)) {
+        s1["round.protonated", i] <- round(as.numeric(s1["protonated", i]), digits = rounder)
+        s1["round.ammoniated", i] <- round(as.numeric(s1["ammoniated", i]), digits = rounder)
+        s1["round.sodiated", i] <- round(as.numeric(s1["sodiated", i]), digits = rounder)
+        s1["round.potassiated", i] <- round(as.numeric(s1["potassiated", i]), digits = rounder)
+        s1["round.deprotonated", i] <- round(as.numeric(s1["deprotonated", i]), digits = rounder)
+        s1["round.chlorinated", i] <- round(as.numeric(s1["chlorinated", i]), digits = rounder)
+        s1["round.acetate", i] <- round(as.numeric(s1["acetate", i]), digits = rounder)
+      }
+
+      library <- cbind(library, s1)
+    }
+  }
+  return(library)
+}
+
+#' Deisotoping
+deisotoping <- function(ppm = 5, no_isotopes = 2, prop.1 = 0.9, prop.2 = 0.5,
+                        spectra = spectra) {
+  C13_1 <- 1.003355
+  C13_2 <- C13_1 * 2
+
+  k <- 0
+  m <- 0
+
+  #' run loop to find isotopes for each ion.
+  for (i in (1:(nrow(spectra) - 1))) {
+    #' values of search
+    mass <- as.numeric(spectra[i, 1])
+    intensity <- as.numeric(spectra[i, 2])
+    #' calculated values
+    offset <- (ppm * mass) / 1000000
+
+    #' find isotope with ppm filter on isotpe
+    search <- round((mass + C13_1), digits = 3)
+    top <- search + offset
+    bottom <- search - offset
+    result <- spectra[as.numeric(spectra[, "intensity"]) <= (intensity * prop.1) & spectra[, 1] >= bottom & spectra[, 1] <= top & spectra[, "isotope"] == "", ]
+    result <- rbind(result, blank1 = "", blank2 = "")
+
+
+    if (no_isotopes == 2) {
+      #' find isotope with ppm filter on isotpe
+      search <- round((mass + C13_2), digits = 3)
+      top <- search + offset
+      bottom <- search - offset
+      result_2 <- spectra[as.numeric(spectra[, "intensity"]) <= (intensity * prop.2) & spectra[, 1] >= bottom & spectra[, 1] <= top & spectra[, "isotope"] == "", ]
+      result_2 <- rbind(result_2, blank1 = "", blank2 = "")
+    }
+
+
+    if (nrow(result) > 2) {
+      k <- k + 1
+      spectra[i, "isotope"] <- paste(spectra[i, "isotope"], " ", "[", k, "]", "[M]", sep = "")
+      for (j in 1:(nrow(result) - 2)) {
+        indices <- which(spectra == result[j, 1], arr.ind = TRUE)
+        spectra[indices[, "row"], "isotope"] <- paste(spectra[indices[, "row"], "isotope"], " ", "[", k, "]", "[M+1]", sep = "")
+      }
+      if (no_isotopes == 2 && nrow(result_2) > 2) {
+        for (j in 1:(nrow(result_2) - 2)) {
+          indices <- which(spectra == result_2[j, 1], arr.ind = TRUE)
+          spectra[indices[, "row"], "isotope"] <- paste(spectra[indices[, "row"], "isotope"], " ", "[", k, "]", "[M+2]", sep = "")
+        }
+      }
+    }
+  }
+
+  allpeaks <- as.data.frame(spectra)
+  deisotoped <- allpeaks[(grep("\\[M\\+", allpeaks$isotope, invert = T)), ]
+  isotopes <- allpeaks[(grep("\\[M\\+", allpeaks$isotope, invert = F)), ]
+  results <- list(allpeaks, deisotoped, isotopes)
+  summary <- paste(length(as.vector(deisotoped$mz.obs)), "monoisotopic peaks retained and", length(as.vector(isotopes$mz.obs)), "C13 isotopes discarded from", length(as.vector(allpeaks$mz.obs)), "detected ions", sep = " ")
+  print(summary)
+  log <- c(log, summary)
+  return(deisotoped)
+}
+
+#' Annotating
+annotating <- function(deisotoped,
+                       adducts = c(H = T, NH4 = F, Na = T, K = F, dH = F, Cl = F, OAc = F),
+                       ppm.annotate = 10, dbase) {
+  print("Starting annotation")
+  d.finalmz <- as.vector(deisotoped$mz.obs)
+  s1 <- dbase
+  spectra <- cbind(round(as.numeric(d.finalmz), digits = 3), d.finalmz)
+  combined <- vector()
+  sel.adducts <- vector()
+  index <- 13 # offset to search only rounded masses in library
+
+  for (a in 1:length(adducts)) {
+    if (adducts[a] == T) sel.adducts <- c(sel.adducts, index + a)
+  }
+
+  for (i in 1:nrow(spectra)) {
+    search <- as.numeric(spectra[i, 1])
+    offset <- (ppm.annotate * search) / 1000000
+    top <- search + offset
+    bottom <- search - offset
+    result <- which(s1[sel.adducts, ] >= bottom & s1[sel.adducts, ] <= top, arr.ind = TRUE)
+    if (nrow(result) > 0) {
+      for (j in 1:nrow(result))
+      {
+        col <- result[j, "col"]
+        row <- result[j, "row"]
+        row <- sel.adducts[row]
+        #' determine the adduct that was matched, summarising match information from library for matched mass (as 'data')
+        #' determine which adduct
+        if (row == "14") {
+          adduct <- "protonated"
+          name.adduct <- "H"
+        }
+        if (row == "15") {
+          adduct <- "ammoniated"
+          name.adduct <- "NH4"
+        }
+        if (row == "16") {
+          adduct <- "sodiated"
+          name.adduct <- "Na"
+        }
+        if (row == "17") {
+          adduct <- "potassiated"
+          name.adduct <- "K"
+        }
+        if (row == "18") {
+          adduct <- "deprotonated"
+          name.adduct <- "-H"
+        }
+        if (row == "19") {
+          adduct <- "chlorinated"
+          name.adduct <- "Cl"
+        }
+        if (row == "20") {
+          adduct <- "acetate"
+          name.adduct <- "OAc"
+        }
+
+        a.ppm <- round(abs(((as.numeric(spectra[i, 2]) - as.numeric(s1[adduct, col])) / as.numeric(spectra[i, 2])) * 1000000), digits = 1)
+
+        #' make vector with summary of match and paired match
+        data <- c(s1[row, col], s1[adduct, col], spectra[i, 2], a.ppm, s1["formula", col], name.adduct, s1["protonated", col], s1["FA1", col], s1["FA2", col], s1["FA3", col])
+
+        #' make matrix of search results
+        combined <- rbind(combined, unlist(data, use.names = F))
+      }
+    }
+  }
+  if (length(combined) > 0) {
+    colnames(combined) <- c("mz.matched", "mz.matched.lib", "mz.observed", "ppm", "formula", "adduct", "mz.lib.protonated", "FA1", "FA2", "FA3")
+
+    ids <- unique.matrix(combined[, c(3, 5, 6)])
+    annotations <- cbind(d.finalmz, "")
+    for (i in 1:nrow(annotations)) {
+      result <- which(ids[, 1] == annotations[i, 1], arr.ind = T)
+      if (length(result) > 0) {
+        for (j in 1:length(result)) {
+          annotations[i, 2] <- paste(annotations[i, 2], "[", ids[result[j], "formula"], "+", ids[result[j], "adduct"], "]", sep = "")
+        }
+      }
+    }
+
+    summary <- paste(length(annotations[annotations[, 2] != "", 2]), "from", length(as.vector(deisotoped$mz.obs)), "monoisotopic peaks were annoated (using accuract mass) with a", ppm.annotate, "ppm tollerance", sep = " ")
+    log <- c(log, summary)
+    print(summary)
+
+    return(annotations[, 2])
+  }
+}
+
+## ==== parameter setting ====
+
+spectra_dir <- "C:/R_lwc/lcms/test-data/lcms_pos" # where your mzML files are stored
+lib_dir <- "C:/R_lwc/lcms/test-data/libraries" # the folder where your library files are stored
+
+FWHM <- 3 # set approximate FWHM (in seconds) of chromatographic peaks
+snthresh <- 5 # set the signal to noise threshold
+minfrac <- 0.25 # minimum fraction of samples necessary for it to be a valid peak group
+profmethod <- "binlin" # use either "bin" (better for centroid, default), "binlin" (better for profile)
+
+adducts <- c(H = T, NH4 = T, Na = T, K = F, dH = F, Cl = F, OAc = F) # choose which adduct you want to include in library search
+ppm.annotate <- 15 # choose ppm for annotations
+ionisation_mode <- "positive" # either "positive" or "negative" - determines which classes of lipids to search for
+
+## ==== Read in library files ====
+setwd(lib_dir)
+
+read <- read.csv("lib_FA.csv", sep = ",", header = T)
+lookup_FA <- read[, 2:4]
+row.names(lookup_FA) <- read[, 1]
+
+read <- read.csv("lib_class.csv", sep = ",", headeq = T)
+lookup_lipid_class <- read[, 2:3]
+row.names(lookup_lipid_class) <- read[, 1]
+
+read <- read.csv("lib_element.csv", sep = ",", header = T)
+lookup_element <- read[, 2:3]
+row.names(lookup_element) <- read[, 1]
+
+read <- read.csv("lib_modification.csv", sep = ",", header = T)
+lookup_mod <- read[, 2:ncol(read)]
+row.names(lookup_mod) <- read[, 1]
+
+FA_expt <- list(
+  "10", "12", "14", "15", "16", "16.1", "17", "17.1", "18", "18.1",
+  "18.2", "18.3", "20.3", "20.4", "20.5", "21", "22", "22.5",
+  "22.6", "24.1"
+)
+
+#' fatty acids to be included in library
+if (ionisation_mode == "positive") {
+  sel.class <- c( #' lipid classes to include - will need to change for negative ion mode
+    T, # TG
+    T, # DG
+    T, # PC
+    F, # PA
+    T, # PE
+    T, # PS
+    F, # PG
+    F, # PI
+    F, # PIP
+    F, # PIP2
+    F, # PIP3
+    T, # LysoPC
+    T, # DG-H20
+    T, # CE
+    F, # FFA
+    T, # SM
+    T # Cer
+  )
+}
+
+if (ionisation_mode == "negative") {
+  sel.class <- c( #' lipid classes to include - will need to change for negative ion mode
+    F, # TG
+    F, # DG
+    T, # PC
+    T, # PA
+    T, # PE
+    T, # PS
+    T, # PG
+    T, # PI
+    T, # PIP
+    T, # PIP2
+    T, # PIP3
+    F, # LysoPC
+    F, # DG-H20
+    F, # CE
+    T, # FFA
+    F, # SM
+    T # Cer
+  )
+}
+
+dbase <- makelibrary(sel.class,
+  fixed = F, fixed_FA, lookup_lipid_class,
+  lookup_FA, lookup_element
+)
+#' wl-15-03-2018: 'fixed_FA' will be one of 'FA_expt'.
+
+## ==== XCMS ====
+
+#' place converted mzML files in working directory
+setwd(spectra_dir)
+path <- paste(getwd())
+files <- list.files(path, recursive = T, full.names = F, pattern = ".mzML")
+
+#' xcms scripts for peak picking and integration
+xset <- xcmsSet(files,
+  method = "matchedFilter", step = 0.1, sigma = FWHM / 2.3548,
+  snthresh = snthresh, profmethod = profmethod
+)
+#' feature recognition and convert group of files to xcms raw object
+
+xset <- group(xset) # groups peaks, temporarily
+#' xset2 <- retcor(xset, family = "symmetric", plottype = "mdevden",
+#'                 smooth = "loess", span = 0.2, missing = 5, extra = 1)
+
+#' corrects retention times
+xset2 <- retcor(xset, method = "obiwarp", profStep = 0.1, plottype = "deviation")
+#' different method for retention time correction - more robust but slower
+
+xset2 <- group(xset2, bw = 5, minfrac = minfrac, mzwid = 0.025)
+#' groups data based on corrected retention times
+
+#' wl-20-05-2019, Mon: save results
+#' save(xset2, file = "C:/R_lwc/lcms/res/xset2_pos.RData")
+#' load("C:/R_lwc/lcms/res/xset2_pos.RData")
+
+#' check for retention time outliers and exclude samples if necessary
+rmsd <- sapply(1:length(xset2@rt$corrected), function(x) {
+  sqrt(sum((xset2@rt$raw[[x]] - xset2@rt$corrected[[x]])**2))
+})
+plot(rmsd)
+
+rmsd <- cbind(files, rmsd)
+write.csv(rmsd, "RT_rmsd.csv")
+
+#' make output based on unique peak groups (mz and RT groups)
+names <- groupnames(xset2, rtdec = 2, mzdec = 4)
+#' define decimal places for mz and RT values
+names <- substr(names, 2, 18)
+
+out <- groupval(xset2, method = "maxint", value = "maxo", intensity = "maxo")
+#' if multiple peaks choose one with highest intensity based on maxo (peak
+#' hieght raw)
+rownames(out) <- names
+out[is.na(out)] <- 0 # replace NAs with 0
+write.csv(out, "xcms_peak_height_raw.csv")
+
+out <- groupval(xset2, method = "maxint", value = "into", intensity = "maxo")
+rownames(out) <- names
+out[is.na(out)] <- 0
+write.csv(out, "xcms_peak_area_raw.csv")
+
+## ==== Peaks without missing value filling ====
+
+#' deisotoping - working with raw peak area - can also change "out" to use
+#' for peak height or the fitered results (value = into/intf/maxo/maxf)
+
+out <- groupval(xset2, method = "maxint", value = "into", intensity = "maxo")
+#' if multiple peaks choose one with highest intensity based on maxo (peak
+#' hieght raw)
+rownames(out) <- names
+out[is.na(out)] <- 0 # replace NAs with 0
+names_split <- colsplit(as.vector(as.character(names)), "T", c("mz", "RT"))
+
+spectra <- cbind(names_split$mz, out[, 1], "", "") #' wl-20-05-2019, Mon: why 1?
+colnames(spectra) <- c("mz.obs", "intensity", "isotope", "modification")
+
+deisotoped <- deisotoping(
+  ppm = 5, no_isotopes = 2, prop.1 = 0.9, prop.2 = 0.5,
+  spectra = spectra
+)
+
+indices <- match(rownames(deisotoped), rownames(out))
+deisotoped_out <- out[indices, ]
+
+names_deiso <- rownames(deisotoped_out)
+names_deiso <- colsplit(as.vector(as.character(names_deiso)), "T", c("mz", "RT"))
+deisotoped_out <- cbind(
+  names_deiso$mz, names_deiso$RT,
+  deisotoped_out[, 1:ncol(deisotoped_out)]
+)
+
+write.csv(deisotoped_out, "xcms_peak_area_raw_deisotoped.csv")
+
+#' annotating
+annotated <- annotating(deisotoped, adducts, ppm.annotate, dbase)
+final_out <- cbind(annotated, deisotoped_out)
+write.csv(final_out, "final_annotated_desiotoped.csv")
+
+#' normalising based on TIC
+data <- read.csv("final_annotated_desiotoped.csv")
+rownames(data) <- data[, 1]
+sums <- as.vector(colSums(data[, 5:ncol(data)], na.rm = T))
+factor <- sums / mean(sums)
+TIC_normalised <- cbind(data[, 2:4], t(t(data[, 5:ncol(data)]) / factor))
+
+write.csv(TIC_normalised, "final_annotated_deisotoped_norm.csv")
+
+#' hist(factor, breaks=100)
+
+## ==== Peaks with missing value filling ====
+
+#' fill in missing peaks by integrating noise
+xset3 <- fillPeaks(xset2) # fills in missing peaks
+names <- groupnames(xset3, rtdec = 2, mzdec = 4)
+#' define decimal places for mz and RT values
+names <- substr(names, 2, 18)
+
+#' deisotope
+out <- groupval(xset3, method = "maxint", value = "into", intensity = "maxo")
+#' if multiple peaks choose one with highest intensity based on maxo (peak hieght raw)
+rownames(out) <- names
+names_split <- colsplit(as.vector(as.character(names)), "T", c("mz", "RT"))
+
+spectra <- cbind(names_split$mz, out[, 1], "", "")
+colnames(spectra) <- c("mz.obs", "intensity", "isotope", "modification")
+
+deisotoped <- deisotoping(
+  ppm = 5, no_isotopes = 2, prop.1 = 0.9, prop.2 = 0.5,
+  spectra = spectra
+)
+
+indices <- match(rownames(deisotoped), rownames(out))
+deisotoped_out <- out[indices, ]
+
+names_deiso <- rownames(deisotoped_out)
+names_deiso <- colsplit(as.vector(as.character(names_deiso)), "T", c("mz", "RT"))
+deisotoped_out <- cbind(
+  names_deiso$mz, names_deiso$RT,
+  deisotoped_out[, 1:ncol(deisotoped_out)]
+)
+
+write.csv(deisotoped_out, "xcms_fill_peak_area_raw_deisotoped.csv")
+
+#' annotate
+annotated <- annotating(deisotoped, adducts, ppm.annotate, dbase)
+final_out <- cbind(annotated, deisotoped_out)
+write.csv(final_out, "final_annotated_desiotoped_fill.csv")
+
+#' normalising based on TIC
+data <- read.csv("final_annotated_desiotoped_fill.csv")
+rownames(data) <- data[, 1]
+sums <- as.vector(colSums(data[, 5:ncol(data)], na.rm = T))
+factor <- sums / mean(sums)
+TIC_normalised <- cbind(data[, 2:4], t(t(data[, 5:ncol(data)]) / factor))
+
+write.csv(TIC_normalised, "final_annotated_deisotoped_fill_norm.csv")
+
+#' hist(factor, breaks=100)
+
+
+#' plot extracted ion chromatograms for each peak group (corrected RT) if
+#' desired, can choose specific samples and/or mz
+
+#' xic.corr <- getEIC(xset3, rt = "corrected", groupidx = 1:nrow(xset3@groups))
+#' plot(xic.corr, xset3, groupidx=1:nrow(xset3@groups), sampleidx=1:length(files))
+
+
diff -r 000000000000 -r 55efed82d7ec lcms/libraries/lib_FA.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/libraries/lib_FA.csv	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,32 @@
+FAname,FAmass,FAcarbon,FAdoublebond
+10,172.1463,10,0
+12,200.1776,12,0
+13,214.1932,13,0
+14,228.2089,14,0
+15,242.2245,15,0
+16,256.2402,16,0
+16.1,254.2243,16,1
+17,270.2558,17,0
+17.1,268.2399,17,1
+17.2,266.2245,17,2
+18,284.2715,18,0
+18.1,282.2558,18,1
+18.2,280.2402,18,2
+18.3,278.2245,18,3
+19.1,296.2709,19,1
+19,298.2866,19,0
+20,312.3028,20,0
+20.1,310.2871,20,1
+20.2,308.2715,20,2
+20.3,306.2558,20,3
+20.4,304.2402,20,4
+20.5,302.2245,20,5
+21,326.3184,21,0
+22,340.3341,22,0
+22.2,336.3028,22,2
+22.4,332.2715,22,4
+22.5,330.2553,22,5
+22.6,328.2396,22,6
+24.1,366.3497,24,1
+16.0L,272.2938,16,0
+0,0,0,0
diff -r 000000000000 -r 55efed82d7ec lcms/libraries/lib_class.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/libraries/lib_class.csv	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,18 @@
+lipid_class,headgroup_mass,FA_number
+TG,41.039125,3
+DG,58.041865,2
+PC,223.09745,2
+PA,138.00825,2
+PE,181.05045,2
+PS,225.0404,2
+PG,212.04505,2
+PI,300.06115,2
+PIP,380.02745,2
+PIP2,459.99375,2
+PIP3,539.96005,2
+LysoPC,240.10019,1
+DG-H20,40.0313,2
+CE,369.3516,1
+FFA,1.007825,1
+SM,166.08675,2
+Cer,1.0312,2
diff -r 000000000000 -r 55efed82d7ec lcms/libraries/lib_element.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/libraries/lib_element.csv	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,13 @@
+element,mass,comment
+H,1.007825,accurate
+C12,12,accurate
+O,15.994915,accurate
+P,30.973763,accurate
+N,14.003074,accurate
+Na,22.98977,accurate
+K,38.963708,accurate
+Li,7.016005,accurate
+NH4,18.034374,accurate
+C13,13.003355,accurate
+Cl,34.968853,isotope 35 (75% abundance)
+CH3COO,59.013305,accurate
diff -r 000000000000 -r 55efed82d7ec lcms/libraries/lib_modification.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/libraries/lib_modification.csv	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,12 @@
+name,type,class,mass
+choline,NL,insource,-59.073499
+phosphocholine,NL,insource,-183.066047
+PE-C2H5N,NL,insource,-43.042199
+phosphoethanolamine,NL,insource,-141.019097
+water,NL,insource,-18.010565
+C13palmitate,label,stableisotope,16.05368
+oxidised,oxidised,biomod,15.994915
+desat.1,desat,biomod,-2.01565
+desat.2,desat,biomod,-4.0313
+desat.3,desat,biomod,-6.04695
+desat.4,desat,biomod,-8.0626
diff -r 000000000000 -r 55efed82d7ec lcms/macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/macros.xml	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,27 @@
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="1.6.4">r-optparse</requirement>
+      <requirement type="package" version="3.6.1">bioconductor-xcms</requirement>
+    </requirements>
+  </xml>
+  <xml name="stdio">
+    <stdio>
+      <regex match="Execution halted"
+            source="both"
+            level="fatal"
+            description="Execution halted." />
+      <regex match="Error in"
+            source="both"
+            level="fatal"
+            description="An undefined error occurred, please check your input
+                          carefully and contact your administrator." />
+      <regex match="Fatal error"
+            source="both"
+            level="fatal"
+            description="An undefined error occurred, please check your input
+                          carefully and contact your administrator." />
+    </stdio>
+  </xml>
+
+</macros>
diff -r 000000000000 -r 55efed82d7ec lcms/test-data/lcms_neg/ZH_180918_mann_neg_001.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/test-data/lcms_neg/ZH_180918_mann_neg_001.mzML	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,16920 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">
+	<cvList count="5">
+		<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>
+		<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>
+		<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>
+		<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>
+		<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+	</cvList>
+	<fileDescription>
+		<fileContent>
+			<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
+		</fileContent>
+		<sourceFileList count="1">
+			<sourceFile id="sf_ru_0" name="ZH_180918_mann_neg_001.raw" location="file:///C:\R_lwc\lcms_neg">
+				<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="c14dc7ee2884b85d08f555b3e62dc433ee1fc4a8" />
+				<cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" />
+				<cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" />
+			</sourceFile>
+		</sourceFileList>
+	</fileDescription>
+	<sampleList count="1">
+		<sample id="sa_0" name="">
+			<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />
+			<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />
+		</sample>
+	</sampleList>
+	<softwareList count="5">
+		<software id="so_in_0" version="2.7.0 SP2" >
+			<cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" />
+		</software>
+		<software id="so_default" version="" >
+			<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />
+		</software>
+		<software id="so_dp_sp_0_pm_0" version="3.0.19199" >
+			<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" />
+		</software>
+		<software id="so_dp_sp_0_pm_1" version="3.0.19199" >
+			<cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" />
+		</software>
+		<software id="so_dp_sp_0_pm_2" version="2.3.0" >
+			<cvParam cvRef="MS" accession="MS:1000757" name="FileFilter" />
+		</software>
+	</softwareList>
+	<instrumentConfigurationList count="1">
+		<instrumentConfiguration id="ic_0">
+			<cvParam cvRef="MS" accession="MS:1001910" name="LTQ Orbitrap Elite" />
+			<cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="SN03037B"/>
+			<componentList count="3">
+				<source order="1">
+					<cvParam cvRef="MS" accession="MS:1000057" name="electrospray inlet" />
+					<cvParam cvRef="MS" accession="MS:1000073" name="electrospray ionization" />
+				</source>
+				<analyzer order="2">
+					<cvParam cvRef="MS" accession="MS:1000014" name="accuracy" value="0" unitAccession="UO:0000169" unitName="parts per million" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000022" name="TOF Total Path Length" value="0" unitAccession="UO:0000008" unitName="meter" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000024" name="final MS exponent" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000025" name="magnetic field strength" value="0" unitAccession="UO:0000228" unitName="tesla" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" />
+				</analyzer>
+				<detector order="3">
+					<cvParam cvRef="MS" accession="MS:1000028" name="detector resolution" value="0" />
+					<cvParam cvRef="MS" accession="MS:1000029" name="sampling frequency" value="0" unitAccession="UO:0000106" unitName="hertz" unitCvRef="UO" />
+					<cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" />
+				</detector>
+			</componentList>
+			<softwareRef ref="so_in_0" />
+		</instrumentConfiguration>
+	</instrumentConfigurationList>
+	<dataProcessingList count="1">
+		<dataProcessing id="dp_sp_0">
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_0">
+				<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />
+			</processingMethod>
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_1">
+				<cvParam cvRef="MS" accession="MS:1000035" name="peak picking" />
+			</processingMethod>
+			<processingMethod order="0" softwareRef="so_dp_sp_0_pm_2">
+				<cvParam cvRef="MS" accession="MS:1001486" name="data filtering" />
+				<cvParam cvRef="MS" accession="MS:1000747" name="completion time" value="2019-10-04+12:48" />
+				<userParam name="parameter: in" type="xsd:string" value="/data/dnb02/galaxy_db/files/011/354/dataset_11354805.dat"/>
+				<userParam name="parameter: in_type" type="xsd:string" value=""/>
+				<userParam name="parameter: out" type="xsd:string" value="/data/dnb02/galaxy_db/files/011/355/dataset_11355132.dat"/>
+				<userParam name="parameter: out_type" type="xsd:string" value=""/>
+				<userParam name="parameter: rt" type="xsd:string" value="500:800"/>
+				<userParam name="parameter: mz" type="xsd:string" value="800:1000"/>
+				<userParam name="parameter: int" type="xsd:string" value=":"/>
+				<userParam name="parameter: sort" type="xsd:string" value="false"/>
+				<userParam name="parameter: log" type="xsd:string" value=""/>
+				<userParam name="parameter: debug" type="xsd:integer" value="0"/>
+				<userParam name="parameter: threads" type="xsd:integer" value="1"/>
+				<userParam name="parameter: no_progress" type="xsd:string" value="false"/>
+				<userParam name="parameter: force" type="xsd:string" value="false"/>
+				<userParam name="parameter: test" type="xsd:string" value="false"/>
+				<userParam name="parameter: peak_options:sn" type="xsd:double" value="0"/>
+				<userParam name="parameter: peak_options:rm_pc_charge" type="xsd:string" value="[]"/>
+				<userParam name="parameter: peak_options:pc_mz_range" type="xsd:string" value=":"/>
+				<userParam name="parameter: peak_options:pc_mz_list" type="xsd:string" value="[]"/>
+				<userParam name="parameter: peak_options:level" type="xsd:string" value="[1, 2, 3]"/>
+				<userParam name="parameter: peak_options:sort_peaks" type="xsd:string" value="false"/>
+				<userParam name="parameter: peak_options:no_chromatograms" type="xsd:string" value="false"/>
+				<userParam name="parameter: peak_options:remove_chromatograms" type="xsd:string" value="false"/>
+				<userParam name="parameter: peak_options:mz_precision" type="xsd:string" value="64"/>
+				<userParam name="parameter: peak_options:int_precision" type="xsd:string" value="32"/>
+				<userParam name="parameter: peak_options:indexed_file" type="xsd:string" value="false"/>
+				<userParam name="parameter: peak_options:zlib_compression" type="xsd:string" value="false"/>
+				<userParam name="parameter: peak_options:numpress:masstime" type="xsd:string" value="none"/>
+				<userParam name="parameter: peak_options:numpress:masstime_error" type="xsd:double" value="0.0001"/>
+				<userParam name="parameter: peak_options:numpress:intensity" type="xsd:string" value="none"/>
+				<userParam name="parameter: peak_options:numpress:intensity_error" type="xsd:double" value="0.0001"/>
+				<userParam name="parameter: spectra:remove_zoom" type="xsd:string" value="false"/>
+				<userParam name="parameter: spectra:remove_mode" type="xsd:string" value=""/>
+				<userParam name="parameter: spectra:remove_activation" type="xsd:string" value=""/>
+				<userParam name="parameter: spectra:remove_collision_energy" type="xsd:string" value=":"/>
+				<userParam name="parameter: spectra:remove_isolation_window_width" type="xsd:string" value=":"/>
+				<userParam name="parameter: spectra:select_zoom" type="xsd:string" value="false"/>
+				<userParam name="parameter: spectra:select_mode" type="xsd:string" value=""/>
+				<userParam name="parameter: spectra:select_activation" type="xsd:string" value=""/>
+				<userParam name="parameter: spectra:select_collision_energy" type="xsd:string" value=":"/>
+				<userParam name="parameter: spectra:select_isolation_window_width" type="xsd:string" value=":"/>
+				<userParam name="parameter: spectra:select_polarity" type="xsd:string" value=""/>
+				<userParam name="parameter: feature:q" type="xsd:string" value=":"/>
+				<userParam name="parameter: consensus:map" type="xsd:string" value="[]"/>
+				<userParam name="parameter: consensus:map_and" type="xsd:string" value="false"/>
+				<userParam name="parameter: consensus:blackorwhitelist:blacklist" type="xsd:string" value="true"/>
+				<userParam name="parameter: consensus:blackorwhitelist:file" type="xsd:string" value=""/>
+				<userParam name="parameter: consensus:blackorwhitelist:maps" type="xsd:string" value="[]"/>
+				<userParam name="parameter: consensus:blackorwhitelist:rt" type="xsd:double" value="60"/>
+				<userParam name="parameter: consensus:blackorwhitelist:mz" type="xsd:double" value="0.01"/>
+				<userParam name="parameter: consensus:blackorwhitelist:use_ppm_tolerance" type="xsd:string" value="false"/>
+				<userParam name="parameter: f_and_c:charge" type="xsd:string" value=":"/>
+				<userParam name="parameter: f_and_c:size" type="xsd:string" value=":"/>
+				<userParam name="parameter: f_and_c:remove_meta" type="xsd:string" value="[]"/>
+				<userParam name="parameter: id:remove_clashes" type="xsd:string" value="false"/>
+				<userParam name="parameter: id:keep_best_score_id" type="xsd:string" value="false"/>
+				<userParam name="parameter: id:sequences_whitelist" type="xsd:string" value="[]"/>
+				<userParam name="parameter: id:accessions_whitelist" type="xsd:string" value="[]"/>
+				<userParam name="parameter: id:remove_annotated_features" type="xsd:string" value="false"/>
+				<userParam name="parameter: id:remove_unannotated_features" type="xsd:string" value="false"/>
+				<userParam name="parameter: id:remove_unassigned_ids" type="xsd:string" value="false"/>
+				<userParam name="parameter: id:blacklist" type="xsd:string" value=""/>
+				<userParam name="parameter: id:rt" type="xsd:double" value="0.1"/>
+				<userParam name="parameter: id:mz" type="xsd:double" value="0.001"/>
+				<userParam name="parameter: id:blacklist_imperfect" type="xsd:string" value="false"/>
+				<userParam name="parameter: algorithm:SignalToNoise:max_intensity" type="xsd:integer" value="-1"/>
+				<userParam name="parameter: algorithm:SignalToNoise:auto_max_stdev_factor" type="xsd:double" value="3"/>
+				<userParam name="parameter: algorithm:SignalToNoise:auto_max_percentile" type="xsd:integer" value="95"/>
+				<userParam name="parameter: algorithm:SignalToNoise:auto_mode" type="xsd:integer" value="0"/>
+				<userParam name="parameter: algorithm:SignalToNoise:win_len" type="xsd:double" value="200"/>
+				<userParam name="parameter: algorithm:SignalToNoise:bin_count" type="xsd:integer" value="30"/>
+				<userParam name="parameter: algorithm:SignalToNoise:min_required_elements" type="xsd:integer" value="10"/>
+				<userParam name="parameter: algorithm:SignalToNoise:noise_for_empty_window" type="xsd:double" value="1e+20"/>
+				<userParam name="parameter: algorithm:SignalToNoise:write_log_messages" type="xsd:string" value="true"/>
+			</processingMethod>
+		</dataProcessing>
+	</dataProcessingList>
+	<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" startTimeStamp="2018-09-18T16:39:03" defaultSourceFileRef="sf_ru_0">
+		<userParam name="mzml_id" type="xsd:string" value="ZH_180918_mann_neg_001"/>
+		<spectrumList count="408" defaultDataProcessingRef="dp_sp_0">
+			<spectrum id="controllerType=0 controllerNumber=1 scan=2019" index="0" defaultArrayLength="38" dataProcessingRef="dp_sp_0">
+				<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000129" name="negative scan" />
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diff -r 000000000000 -r 55efed82d7ec lcms/test-data/lcms_neg/ZH_180918_mann_neg_002.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/test-data/lcms_neg/ZH_180918_mann_neg_002.mzML	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,16920 @@
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diff -r 000000000000 -r 55efed82d7ec lcms/test-data/lcms_pos/ZH_190918_mann_liver_pos_001.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/test-data/lcms_pos/ZH_190918_mann_liver_pos_001.mzML	Tue Oct 22 04:19:31 2019 -0400
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+				<userParam name="parameter: algorithm:SignalToNoise:write_log_messages" type="xsd:string" value="true"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
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+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="14720387"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
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+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
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+					</scan>
+				</scanList>
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
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+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2009.59518114498" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000796" name="spectrum title" value="ZH_190918_mann_liver_pos_001.1054.1054. File:&quot;ZH_190918_mann_liver_pos_001.raw&quot;, NativeID:&quot;controllerType=0 controllerNumber=1 scan=1054&quot;"/>
+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="516.3171" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="12224">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
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+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
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+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
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Ub/RotAK3ppxwRWi0DZUIgbEFaLQFkyrm8bVotArTzVFFRWi0DBxB9mgVaLQI0TjLqMVotAY23/DphWi0BULfAeDFqLQKU4kHUXWotA2FA3zCJai0DhMhonUFqLQNlhTYJ9WotAAe8z2Yhai0BAiSEwlFqLQL+jagEJXotA1JGFWhRei0DajqezH16LQMtgu3FYXotA9ODU1oVei0CXdD0wkV6LQG8XrYmcXotA1zIR3TJmi0C5XkA7PmaLQL2ddplJZotAV6tQz41mi0BXStdIu2aLQItdW6fGZotAKITmBdJmi0CFKJ3tjW6LQDr4/1CZbotAZ99ptKRui0A2Z1hC0m6LQFy9fND/botAyXgmNAtvi0DkS9eXFm+LQDvxF9vxdYtA8TMVQ/11i0DvkRmrCHaLQFAbcks2dotANXit62N2i0DczPFTb3aLQAs9Pbx6dotAjLoKNZ+Hi0AMRA2oqoeLQP3xFhu2h4tAxRaF5+OHi0Cn2E+0EYiLQLXPmScdiItAdevqmiiIi0BUU0rmQoqLQDxr8lpOiotA96ihz1mKi0C6FXkXk4qLQIZyn1/MiotA1VGd1NeKi0A9V6JJ44qLQE4A9M+glotA6VFUTKyWi0DEz7vIt5aLQIzdLDfxlotAZybiKB+Xi0D/X5GlKpeLQB3GRyI2l4tAURzHmGCui0BeZ/8jbK6LQAnrPq93rotAbc/oZ7Gui0Copn2V366LQMdhBSHrrotAylWUrPaui0DOaCzTi7aLQDE7gWOXtotAcUrd86K2i0DH6JU10baLQB32Q3f/totAXSrhBwu3i0C/m4WYFreLQI7lI+UnxotAyD4/fzPGi0AK3WEZP8aLQOMAfBx5xotAYAPHH7PGi0C0mjm6vsaLQFd3s1TKxotAkqQNtqLWi0Cf/n1artaLQFam9f651otAiU4dkejWi0B2nzjIIteLQFFR+Wwu14tAHVHBETrXi0Ca0jI+392LQPGXLefq3YtAvq4vkPbdi0De56fdMN6LQKDMEYJf3otAkBNdK2vei0A/rK/Udt6LQMCR5IcE7YtAQidiOhDti0A1FufsG+2LQOdQRLdK7YtAoejNgXnti0Cp/ZQ0he2LQFlsY+eQ7YtATOUbxRL2i0Asfkp9HvaLQEF1gDUq9otAKgCiFln2i0Bw1Lf3h/aLQIYcMLCT9otAC8OvaJ/2i0Al632yEwaMQCmwvXQfBoxA0tsENysGjEDgutcCZgaMQPlsBXKeBoxAeAOeNKoGjEDmAD73tQaMQFFl5bnBBoxAvDCUfM0GjECRM21KCAeMQO6v3DhRB4xAMVHk+1wHjEDBWfO+aAeMQDyofcgKFoxAOEbLlBYWjEBNUyBhIhaMQAUYOV9dFoxA24LKXZgWjECkV3EqpBaMQM6bH/evFoxAsYMh/SgejEAX+4zONB6MQOfl/59AHoxAnBMW5m8ejECkRoEsnx6MQCRBN/6qHoxASK/0z7YejEAzTW3lXCKMQB0uf7loIoxAqYSYjXQijECaGoeyryKMQLygtgPfIoxA4JAa2OoijEDt9oWs9iKMQOYakiELJYxArMpU9xYljEB58R7NIiWMQB+ugfpdJYxA/9aoro8ljEClpb2EmyWMQJzr2VqnJYxAGU+PuR0mjEAut/2PKSaMQOCWc2Y1JoxAQqbTbXwmjEDea9sZwSaMQL5gsvDMJoxAl82Qx9gmjEBAQYH4yS2MQEeJyNPVLYxA+UwXr+EtjEA0MZ0cES6MQHKbl4pALoxAMQm91HsujED9SVzXzi6MQAO8HUf+LoxA+5snIwovjEBH+Dj/FS+MQKIA0cjdMYxAmCurpukxjEBu1IyE9TGMQEmBZdowMoxA2pEVv1QyjECBqDqdYDKMQEM9Z3tsMoxADPE41TRWjEB2gAvKQFaMQBqh5b5MVoxAqWmwcaBWjECdSTna81aMQH3vhM//VoxA9ibYxAtXjEDQe4QaXVqMQDTp+BFpWoxACep0CXVajEBBsLDnpFqMQHZqRcbUWoxAXZsFvuBajED0X8217FqMQAA/vK1WXoxA2Pm0p2JejEBBSrWhbl6MQJagKISqXoxAvNAYZ+ZejED8j2xh8l6MQBrlx1v+XoxAAR6NVVhmjED/K5hUZGaMQNXTqlNwZoxAjR96T6xmjEAwtYpL6GaMQP368Er0ZoxA79peSgBnjEDl42Bn1XWMQCmXPXDhdYxAk+whee11jEAomP+cHXaMQOTS5txxdoxAVmd2AaJ2jEB/4tQKrnaMQD8AOxS6doxAI9YbYLaJjEAGmJZ1womMQMAGGYvOiYxAZIJv4f6JjEA7/Rs3L4qMQIOA40w7ioxA37CyYkeKjEDN0/rk9K2MQA8ighEBroxAsjARPg2ujEBp75rwPa6MQAxNO6NuroxAJiAQ0HqujEDfs+z8hq6MQJxN+Ld6uoxAYLN57Ia6jEBE4AIhk7qMQNVbdfPDuoxAEUkI+wC7jEDRPt8vDbuMQAD8vWQZu4xAFA1cbdK/jEBWM0Wl3r+MQKUjNt3qv4xAm6xf9SfAjEBHkffVWMCMQF5nNg5lwIxAxQd9RnHAjED3CyXXfsKMQBuMwhCLwoxAuNdnSpfCjECW+UoxyMKMQHGh91EFw4xAWOHqixHDjEAE7eXFHcOMQJbvQBod1oxA4tNiYCnWjEBSjoymNdaMQFu/0gVz1oxAdiTEHqDWjEClPTxlrNaMQEUtvKu41oxAvObeGDXejEDnmS5kQd6MQJsnhq9N3oxAPbuxKIvejEBdquWizN6MQMqdk+7Y3oxADmxJOuXejEBNIgr7leGMQKbWf0ii4YxAYmf9la7hjECNJecZ7OGMQBoHxlAd4oxA0OoliE7ijEBbzWW/f+KMQEvhcA2M4oxAG9KDW5jijEBuGMjekfWMQEjYBDme9YxAaH9Jk6r1jEARJav82/WMQA0xqBsm9oxA1iIChlf2jEAhWr3gY/aMQBd5gDtw9oxArov2QkP+jEBMkMOiT/6MQO6AmAJc/oxAGnw7go3+jECiy50Bv/6MQJcJumHL/oxAzjPewdf+jEDPqeS09BWNQJrZ3yMBFo1AYgLjkg0WjUDUXz9PPxaNQPWR5Hp9Fo1AA3Y36okWjUBcU5JZlhaNQJy8MGECJo1As4h42g4mjUCXVshTGyaNQJCgVzlNJo1AYjWkHn8mjUCdFDyYiyaNQOH12xGYJo1AOhwTyRY+jUCFE9NRIz6NQNcZm9ovPo1AHBz8hm4+jUCAp+gzrT6NQBpVCb25Po1ADBIyRsY+jUBkLlIoyEWNQEKqBLbURY1Abzm/Q+FFjUCDN/p6E0aNQES3PEBSRo1AyghIzl5GjUDgbVtca0aNQDhhm5xAVY1Ab9RCNE1VjUCAY/LLWVWNQJe2ASuMVY1AHPKMir5VjUDffIUiy1WNQLwjhrrXVY1A28Wf6vBVjUAwwbiC/VWNQLfY2RoKVo1Ah/b4E0lWjUCIpAojdlaNQK3XfLuCVo1AVyf3U49WjUCNroLb1leNQEUK2HTjV41APoM1DvBXjUA7mIINL1iNQN8Kkvl/WI1APeVQk4xYjUA/3RctmViNQFi7Lk6RWo1AcYlC6Z1ajUBXdl6EqlqNQEblY4zpWo1Ad5ax+RtbjUCPuB6VKFuNQLP5kzA1W41ATTitMTpdjUD5qnfORl2NQOg9SmtTXY1AIwHhe5JdjUCopRS1xF2NQIN8OFLRXY1A43Nk791djUDaM18cQGaNQEt5+r5MZo1A/uOdYVlmjUD9KEmPmGaNQBadIr3XZo1ANaMfYORmjUDnziQD8WaNQAWDMAXfdY1AkBPfset1jUAC0pVe+HWNQLc7or43do1AJnsqH3d2jUBaNDvMg3aNQMobVHmQdo1AIXZM7OV9jUDweSme8n2NQBuwDlD/fY1AWLMDyj5+jUDR9SzeZH6NQIDyW5Bxfo1AziGTQn5+jUCi1sfTvrWNQAgVxanLtY1A76TKf9i1jUBlFDTYC7aNQHKiOy8/to1ATxGMBUy2jUD+0eTbWLaNQMTlBf8O5o1AaC1f9BvmjUC14cDpKOaNQBLym79c5o1AVIWZlZDmjUDgDEeLneaNQFkB/YCq5o1ATLZlTP3vjUBlUTRICvCNQL1eC0QX8I1AclS9L1jwjUBuAfwfjPCNQPyGJxyZ8I1AHX9bGKbwjUC8jYqbrfKNQCr4GJm68o1AYdavlsfyjUCO1V+N+/KNQAX5XoI8841AlV5KgEnzjUBCOD5+VvONQHNhbUde9Y1AqOu7Rmv1jUAs6xJGePWNQMt+w0Os9Y1A8h+TQe31jUAHtj5B+vWNQLTB8kAH9o1AN9zDP3z2jUCfgcw/ifaNQPSc3T+W9o1Ahg+yQNf2jUBwRrhAC/eNQJ/+HUEY941AES2MQSX3jUDYG5LY3BWOQEnQC+3pFY5AZAyOAfcVjkBQSuxTKxaOQIOtMKZfFo5AFbD/umwWjkCoOtfPeRaOQHH831zuJY5ATbDVe/sljkD49NOaCCaOQGTJSzZKJo5AVwLW5IomjkDOgTIEmCaOQG2SlyOlJo5ANTQFQ7ImjkAB4Kng8yaOQIsqZoxDJ45A0pw6rFAnjkCuoBfMXSeOQPhHsT66LY5A6kS+YsctjkAc19OG1C2OQN70fxcJLo5AbY3FzEoujkCf9TDxVy6OQFvzpBVlLo5AYFrdR+U1jkBjd0Bx8jWOQE8urJr/NY5AMsZHakE2jkCww5E6gzaOQEgZXGSQNo5AIgkvjp02jkCLxNd09TmOQO244qACOo5Agkn2zA86jkBoppp9RDqOQJ3I/C+FOo5Az3RmXJI6jkCMvdiInzqOQE9egSECRo5ADTpuVQ9GjkDfuGOJHEaOQA3CsI1eRo5AFtXq8K5GjkAX+0clvEaOQIjErVnJRo5AscJUHxpejkC28wZjJ16OQI3VwaY0Xo5AgZzq+XZejkDo8k5NuV6OQPpvaZHGXo5AO56M1dNejkCC8PgDxm2OQLkF8VHTbY5Aw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diff -r 000000000000 -r 55efed82d7ec lcms/test-data/lcms_pos/ZH_190918_mann_liver_pos_002.mzML
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/test-data/lcms_pos/ZH_190918_mann_liver_pos_002.mzML	Tue Oct 22 04:19:31 2019 -0400
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="500.61259999998" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="11288">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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Cs2A4tA9YQATEEDi0DYqtNsTAOLQGdzlmHSIItAx9uzlN0gi0CtM9jH6CCLQMLpQ/srIYtA2yytMWEhi0B/wCRlbCGLQO5Do5h3IYtAqkBm4tIii0A7ycIW3iKLQFNCJkvpIotAfbh/USEji0CnK0J2YiOLQNrs+KptI4tA2Z6233gji0DiV40aySSLQHQ+IlDUJItAjRa+hd8ki0A04GC76iSLQK749sciJYtA56XljHMli0DhteLCfiWLQLu35viJJYtA8FAoI88mi0BptfxZ2iaLQHEM2JDlJotA2/2N2igni0Bgt12KbieLQNdhk8F5J4tAMv/P+IQni0DLHJ624CiLQDUiue7rKItAQRvbJvcoi0CNP+0/LymLQMLQ74lnKYtAIENewnIpi0BjqdP6fSmLQHL+1xflKotAt+EyUfAqi0CeuZSK+yqLQEioYXAoK4tABLm/jmAri0C4IGfIayuLQFJ9FQJ3K4tAjez2ekRai0AZFbrRT1qLQKhKhChbWotARqPzg4hai0CexbTftVqLQChxvjbBWotA6inPjcxai0BhBz1eH16LQO3vZbcqXotAeeeVEDZei0DwW5x1Y16LQO2RMS+MXotAWBGhiJdei0D6nxfiol6LQPyZuAHghItADHwHc+uEi0AngV3k9oSLQACpdhswhYtASuQ7O3eFi0Cmj+esgoWLQFNemh6OhYtA3O3xxIWHi0DHCuY3kYeLQB9M4aqch4tA8NFaXeGHi0A1OGVvJYiLQO5UveIwiItAXpYcVjyIi0C6QR1GNIqLQA8Qvro/iotANwRmL0uKi0Au2Ovrj4qLQL/inwfOiotAZcSkfNmKi0AnzLDx5IqLQKDEtqHojItAN78LGPSMi0AF4WeO/4yLQBLXn944jYtAAvzKpnuNi0C6znUdh42LQPDIJ5SSjYtA6upejpaPi0AJF1oGoo+LQMJrXH6tj4tA/HTT1uaPi0Bv4TIPHJCLQCj2g4cnkItAwTPc/zKQi0Dh6sL355SLQIuYEnPzlItAj3Fp7v6Ui0DnOYdXOJWLQEiRRWt+lYtAcHTy5omVi0BGg6ZilZWLQIcDx+7tlotAgWdZa/mWi0Dh9/LnBJeLQMlkXlc+l4tAbFvUxHmXi0Dd1bxBhZeLQPp8rL6Ql4tAdLPKb+mYi0CPz5jt9JiLQBgZbmsAmYtAy40EX0WZi0CBM0LKf5mLQBygbUiLmYtAcTqgxpaZi0D82Zid75qLQOIJqhz7motAQ2jCmwabi0BI+qcXQJuLQAXPMJR5m4tAUC6YE4Wbi0BgvAaTkJuLQO4MVQ/1nItA7n+pjwCdi0B5IgUQDJ2LQBAZO5JFnYtAdL+0knOdi0CqPlgTf52LQK/tApSKnYtAT4IMZP/Vi0D8ehYIC9aLQAXBJ6wW1otAFt+1PEXWi0CZ6jPMc9aLQNTphnB/1otApDbhFIvWi0B/BUcdHwaMQHUMjt8qBoxAHXrcoTYGjEADNGCrZQaMQLnNQrWUBoxAmNjTd6AGjEBkSmw6rAaMQFRKJCUECYxAj8U96Q8JjEADqV6tGwmMQEE2coJWCYxAZr0uWJEJjEC/HKEcnQmMQJ3kGuGoCYxA1Yd9L/4KjEAJmtX0CQuMQH0VNboVC4xAZqqBlVALjEBS6GKWiguMQC3rE1yWC4xAlFfMIaILjED1ZEmU9wyMQA074FoDDYxAbXt+IQ8NjEBmt8/JVQ2MQG3MOIeRDYxATAowTp0NjEDMsi4VqQ2MQM2Sf3QKD4xAeDBkPBYPjECDOVAEIg+MQJGyW+xcD4xAxtFEUIYPjEAeDnsYkg+MQCC2uOCdD4xA4m1tZf8QjEB7K5EuCxGMQIlVvPcWEYxAQoMD5lERjECti90skRGMQC5gWvacEYxAcKHev6gRjECBzud8oR+MQOqZQU+tH4xAfdmiIbkfjEAt4IYQACCMQOh/4fc2IIxAkDOcykIgjEC9W16dTiCMQBP3iB9LIoxAdT2T81YijEB1+aTHYiKMQG8IrMCpIoxAP/PWs/QijEBMqkmIACOMQEfXw1wMI4xAnYUhU/0kjEBrmdwoCSWMQEEkn/4UJYxAl9TbK1AljEDlWa4KmCWMQOt6yuCjJYxARhPutq8ljEC1CIHKrCeMQGw87aG4J4xAkehgecQnjEDpVBOv/yeMQMTcMoNHKIxALjAAW1MojEBh/NQyXyiMQJCvc0F0KoxAh0mgGoAqjEBkXdTziyqMQJZw71i7KoxAd4GLbuwqjEC23wJI+CqMQCW4gSEEK4xASfyuAwtVjEAUQMT3FlWMQHsU4esiVYxAt+wspWpVjEAY0G65pFWMQI5t5q2wVYxA7ptlorxVjECNEmP8Hl2MQC2AlvUqXYxAsoLR7jZdjEB0XgnUZl2MQM1WqrmWXYxAqJYps6JdjECxa7Csrl2MQHzAtfIhX4xA5Ecv7S1fjEBQZbDnOV+MQFm3ANJpX4xAK2C3vJlfjECZxHy3pV+MQEa/SbKxX4xAIsqtAnlhjECbu6L+hGGMQE5En/qQYYxABlDd6sBhjECWYbXa8GGMQJA89tb8YYxACq8+0whijEBE2PjPH32MQLK/dd0rfYxANE366jd9jEBTAFkhaH2MQI8h22WkfYxADC2sc7B9jEDc3oSBvH2MQH8aBaUUgYxACtcEtSCBjEDKOwzFLIGMQCEPpBVpgYxA5K7oZqWBjEBQT0R3sYGMQD6Yp4e9gYxA3wOL6W+DjECluAn7e4OMQNkWkAyIg4xAvy72UriDjEDeSV2Z6IOMQEOeKKv0g4xAYpz7vACEjEA2vROmf5KMQMmfI8GLkoxA7TM73JeSjECFdOZIyJKMQPx6WPn3koxAQE61FASTjEBS0xkwEJOMQHmT8jlhuoxA7URkbm26jEB8vd2iebqMQCbnWd7CuoxA6C6pFf26jECQ/n9KCbuMQKWVXn8Vu4xAOsAvEQq9jECFJlVHFr2MQFVVgn0ivYxAuky3sy69jED/4jTDa72MQKTapt++vYxAsgNBFsu9jECo9eJM172MQDWDIe+/v4xAVrkCJ8y/jEB1uete2L+MQDGR7XYVwIxAAP9LXGHAjEBCeZKUbcCMQOK94Mx5wIxAooae627CjEAqFTQle8KMQCdv0V6HwoxA3B1Zf8TCjECsMrGsEMOMQDAYrOYcw4xAe8muICnDjECR2laFHsWMQKoSocAqxYxArhfz+zbFjEBGMwIldMWMQINRb9OxxYxAOSYXD77FjEAryMZKysWMQO8oLfIt8YxAKPuaSTrxjEBDshChRvGMQOt/Nv938YxAvmuEtbXxjEADFUkNwvGMQGyjFWXO8YxA7bVk0orzjEDPdVUrl/OMQNwbToSj84xAI7J/6NTzjEAcKyJNBvSMQMrpYaYS9IxA346p/x70jEByNKtZIvWMQIitoLMu9YxAqA2eDTv1jEBvQzQqhfWMQGOeeu3C9YxA69TWR8/1jEDN8jqi2/WMQNUcdjYp94xA2ZO3kTX3jED+8gDtQfeMQKZp5rV/94xArEeBf733jEANoiHbyfeMQOTkyTbW94xAsUa8STD5jEAc6kmmPPmMQMV23wJJ+YxAmeFB0ob5jEB1+wOgxPmMQIiP8PzQ+YxAKQ3lWd35jEBVvGW4PUWNQLA+v0VKRY1ACNQg01ZFjUDJ5/cIiUWNQIYCCD+7RY1A+UOyzMdFjUCqmGRa1EWNQCBqpj0sTo1APCq/0DhOjUBIAuBjRU6NQDBStLB3To1A7nvvQaVOjUB3LFnVsU6NQDH1ymi+To1AG0qO7S5VjUA8ei2FO1WNQCbG1BxIVY1Ay+OSE4dVjUCOlGQqxlWNQB4UZcLSVY1AyK9tWt9VjUAXVcE111eNQH2JFs/jV41AI9tzaPBXjUCDK8BnL1iNQD686dWIWI1A7Yywb5VYjUBDe38JoliNQJi9tfWAWo1AokXBkI1ajUBl7NQrmlqNQCpc9c7lWo1Agg3kTS5bjUBsRmHpOluNQHSe5oRHW41Aiv72TjNdjUDZScHrP12NQGy1k4hMXY1A07MpmYtdjUBft7HO3V2NQPin5WvqXY1AKLkhCfddjUA+Co6071+NQFlrF1P8X41AMu6o8QhgjUB8d/oKSGCNQKgVNkt6YI1AZ+sY6oZgjUA24wOJk2CNQAoDvno8Z41ACQ/8HUlnjUDMQELBVWeNQG9xG/KUZ41AqIsUgMdnjUDMOKwj1GeNQAcMTMfgZ41A6PMvFTZpjUCo/LO5QmmNQE8sQF5PaY1AtGJ3lY5pjUA77WXNzWmNQFvKS3LaaY1At845F+dpjUAsjV6IPGuNQH/mMC5Ja41Az2cL1FVrjUBwR8oRlWuNQD4TT0/Ua41Aa06D9eBrjUDmsb+b7WuNQCdoxnZKhY1AlsRpLVeFjUCGVxXkY4WNQIzEFb+WhY1AXH/MmcmFjUDR/cFQ1oWNQAazvwfjhY1AdYZ6uqSZjUD48UV+sZmNQEqfGUK+mY1AP+e6UfGZjUB/iCthJJqNQGiHSSUxmo1AZMhv6T2ajUCwhfpnk6uNQOA7YTegq41A6z3QBq2rjUDuPN9E4KuNQEDFX1EgrI1AI78hIS2sjUAoBezwOayNQIXBWTZR2Y1AEHZrI17ZjUAWkIUQa9mNQJnvQcWe2Y1ANxdcetLZjUDpw8Fn39mNQF7WL1Xs2Y1Ashm+w07djUBdd2ezW92NQL08GaNo3Y1AtSwQUqndjUBG3sQB6t2NQJ4a0/H23Y1ABr/p4QPejUBrgb1PVN+NQJsqt0Bh341Arzy5MW7fjUAcvUHnrt+NQELXMazi341AnwOIne/fjUAnmeaO/N+NQAg5lgJn4Y1AVcXo9HPhjUCnu0PngOGNQPK5A7G04Y1AJxOP8eXhjUAcxTXk8uGNQGjh5Nb/4Y1AfFrOZfrvjUAQzZxhB/CNQOGxc10U8I1A+dwkSVXwjUDjkI0kk/CNQH1gwSCg8I1ArqL9HK3wjUCYS2SmmvKNQLYZ6qOn8o1Am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+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="11020">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
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+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
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+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
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+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
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+					</scan>
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+				<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+				<cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="388.393981933594" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="1563982" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="14471415"/>
+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="110.000039334922" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2009.59503040427" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="519.2424" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
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+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="11256">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="15224186"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="528.0675" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="13024">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="11960">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="13900">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
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+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
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+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				</scanList>
+				<binaryDataArrayList count="2">
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
+					<binaryDataArray encodedLength="11980">
+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="110.00015877279" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2009.59516679736" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000796" name="spectrum title" value="ZH_190918_mann_liver_pos_002.1099.1099. File:&quot;ZH_190918_mann_liver_pos_002.raw&quot;, NativeID:&quot;controllerType=0 controllerNumber=1 scan=1099&quot;"/>
+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="538.3626" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
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+						<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+						<cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" />
+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+						<cvParam cvRef="MS" accession="MS:1000576" name="no compression" />
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+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
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+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="15662481"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="540.3237" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
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+				<cvParam cvRef="MS" accession="MS:1000127" name="centroid spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />
+				<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" />
+				<cvParam cvRef="MS" accession="MS:1000130" name="positive scan" />
+				<cvParam cvRef="MS" accession="MS:1000504" name="base peak m/z" value="388.394439697266" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000505" name="base peak intensity" value="2244154.5" unitAccession="MS:1000131" unitName="number of detector counts" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="15285877"/>
+				<cvParam cvRef="MS" accession="MS:1000528" name="lowest observed m/z" value="110.000036754777" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
+				<cvParam cvRef="MS" accession="MS:1000527" name="highest observed m/z" value="2009.59505357132" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="540.81430000002" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+								<cvParam cvRef="MS" accession="MS:1000500" name="scan window upper limit" value="2000" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
+							</scanWindow>
+						</scanWindowList>
+					</scan>
+				</scanList>
+				<binaryDataArrayList count="2">
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+				<cvParam cvRef="MS" accession="MS:1000285" name="total ion current" value="11666118"/>
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+				<userParam name="filter string" type="xsd:string" value="FTMS + p ESI Full ms [110.00-2000.00]"/>
+				<userParam name="preset scan configuration" type="xsd:string" value="1"/>
+				<scanList count="1">
+					<cvParam cvRef="MS" accession="MS:1000795" name="no combination" />
+					<scan >
+						<cvParam cvRef="MS" accession="MS:1000016" name="scan start time" value="542.286" unitAccession="UO:0000010" unitName="second" unitCvRef="UO" />
+						<userParam name="MS:1000927" type="xsd:double" value="10"/>
+						<scanWindowList count="1">
+							<scanWindow>
+								<cvParam cvRef="MS" accession="MS:1000501" name="scan window lower limit" value="110" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
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+							</scanWindow>
+						</scanWindowList>
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+				</scanList>
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diff -r 000000000000 -r 55efed82d7ec lcms/test-data/res/peak_neg.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/test-data/res/peak_neg.tsv	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,8 @@
+"annotated"	"mz"	"rt"	"ZH_180918_mann_neg_001"	"ZH_180918_mann_neg_002"
+"No annotations were made"	821.0043	542.96	52735.7602380384	56650.6423116565
+"No annotations were made"	837.0347	543.45	39379.4895999942	47394.1692802245
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+"No annotations were made"	961.0504	542.59	106250.185945129	117415.913502999
diff -r 000000000000 -r 55efed82d7ec lcms/test-data/res/peak_pos.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lcms/test-data/res/peak_pos.tsv	Tue Oct 22 04:19:31 2019 -0400
@@ -0,0 +1,18 @@
+"annotated"	"mz"	"rt"	"ZH_190918_mann_liver_pos_001"	"ZH_190918_mann_liver_pos_002"
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+""	970.7472	542.79	38192.9323318229	11319.4007267118
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diff -r 000000000000 -r 55efed82d7ec lcms/test-data/res/xset_neg.rdata
Binary file lcms/test-data/res/xset_neg.rdata has changed
diff -r 000000000000 -r 55efed82d7ec lcms/test-data/res/xset_pos.rdata
Binary file lcms/test-data/res/xset_pos.rdata has changed