# HG changeset patch # User galaxyp # Date 1631252492 0 # Node ID 65ce27f0fa0155ea371e2838486cec1a9a764ed5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification commit 2535f45b8a0f617a0525a88c195602a6a3978152" diff -r 000000000000 -r 65ce27f0fa01 proteomiqon_psmbasedquantification.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteomiqon_psmbasedquantification.xml Fri Sep 10 05:41:32 2021 +0000 @@ -0,0 +1,385 @@ + + + allows label-free quantification as well as quantification of full metabolic labeled samples. + + + 0.0.7 + + + proteomiqon-psmbasedquantification + + > '$out_paramfile' && + #end if + ln -s '$instrumentOutput' '${instrumentOutput_basename}.mzlite' && + ln -s '$scoredPSMs' '${scoredPSMs_basename}.qpsm' && + ln -s '$peptideDB' '${peptideDB_basename}.db' && + ln -s '$out_quant' '${instrumentOutput_basename}.quant' && + proteomiqon-psmbasedquantification -i './${instrumentOutput_basename}.mzlite' -ii './${scoredPSMs_basename}.qpsm' -d './${peptideDB_basename}.db' -p '$paramfile' -o ./ + ]]> + + + + + + + + + + + +

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+ + + + + + + + + + `_ and `peptide spectrum matches `_ which `passed fdr thresholds `_. + +Once a MS/MS spectrum is mapped to a peptide sequence the quantity of the fragmented peptide ion comes into view. + +Given an MS run in the mzLite or mzml format and a list of fdr controlled peptide spectrum matches, this tool iterates accross all identified MS/MS scans and groups them by the assigned peptide ion. +The scan times of each MS/MS spectrum are then weighted according to the quality of each match to build an reliable estimator for the scan time of the peptide ion in question. +This scan time estimator, combined with the monoisotopic m/z, is then used to extract an ion chromatogram. +Using wavelet based peak detection techniques we identify all peaks present in the XIC and select the most probable peak our target for quantification. +Using parameter estimation techniques we subsequently use peak fitting to fit a set of two gaussian models to the detected peak, from whom the one with the better fit is selected. +This allows us not only to report how well the signal fitted to the theoretical expected peak shape but also to obtain accurate estimates for the peak area, our estimator for peptide ion abundance. + +.. image:: LabeledQuant.png + :width: 768pt + :height: 228pt + +The quantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples. +For this we use the known identity of one of the the peptide ions and calculate the m/z of the unobserved differentially labeled counterpart to extract and quantify the corresponding XIC. + +Further Reading +--------------- +Additional information about the tool can be found in the `documentation `_. + ]]> + + diff -r 000000000000 -r 65ce27f0fa01 static/images/LabeledQuant.png Binary file static/images/LabeledQuant.png has changed diff -r 000000000000 -r 65ce27f0fa01 test-data/result_1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_1.json Fri Sep 10 05:41:32 2021 +0000 @@ -0,0 +1,43 @@ + + + { + "PerformLabeledQuantification": true, + "XicExtraction": + { + "ScanTimeWindow": 2.0, + "MzWindow_Da": { + "Case": "Fixed", + "Fields": [ + 0.07 + ] + }, + "XicProcessing": { + "Case": "SecondDerivative", + "Fields": [ + { + "MinSNR": 2.0, + "PolynomOrder": 2, + "WindowSize": { + "Case": "Fixed", + "Fields" : [ + 11 + ] + } + } + ] + }, + "TopKPSMs": null + }, + "BaseLineCorrection": { + "Case": "Some", + "Fields": [ + { + "MaxIterations":10, + "Lambda":6, + "P":0.05 + } + ] + } + } + + \ No newline at end of file diff -r 000000000000 -r 65ce27f0fa01 test-data/result_2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_2.json Fri Sep 10 05:41:32 2021 +0000 @@ -0,0 +1,54 @@ + + + { + "PerformLabeledQuantification": true, + "XicExtraction": + { + "ScanTimeWindow": 2.0, + "MzWindow_Da": { + "Case": "Estimate", + }, + "XicProcessing": { + "Case": "Wavelet", + "Fields": [ + { + "Borderpadding": { + "Case": "Some", + "Fields": [ + 2 + ] + }, + "BorderPadMethod": { + "Case": "Random" + }, + "InternalPaddingMethod": { + "Case": "LinearInterpolation" + }, + "HugeGapPaddingMethod": { + "Case": "Zero" + }, + "HugeGapPaddingDistance": 100.0, + "MinPeakDistance": null, + "MinPeakLength": { + "Case": "Some", + "Fields": [ + 0.1 + ] + }, + "MaxPeakLength": 1.5, + "NoiseQuantile": 0.01, + "MinSNR": 0.01, + } + ] + }, + "TopKPSMs": { + "Case": "Some", + "Fields": [ + 3 + ] + } + }, + "BaseLineCorrection": null + } + + \ No newline at end of file diff -r 000000000000 -r 65ce27f0fa01 test-data/result_3.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_3.json Fri Sep 10 05:41:32 2021 +0000 @@ -0,0 +1,44 @@ + + + { + "PerformLabeledQuantification": true, + "XicExtraction": + { + "ScanTimeWindow": 2.0, + "MzWindow_Da": { + "Case": "Estimate", + }, + "XicProcessing": { + "Case": "Wavelet", + "Fields": [ + { + "Borderpadding": null, + "BorderPadMethod": { + "Case": "Zero" + }, + "InternalPaddingMethod": { + "Case": "Zero" + }, + "HugeGapPaddingMethod": { + "Case": "Delete" + }, + "HugeGapPaddingDistance": 101.0, + "MinPeakDistance": { + "Case": "Some", + "Fields": [ + 2.0, + ] + }, + "MinPeakLength": null, + "MaxPeakLength": 1.5, + "NoiseQuantile": 0.01, + "MinSNR": 0.01, + } + ] + }, + "TopKPSMs": null + }, + "BaseLineCorrection": null + } + + \ No newline at end of file diff -r 000000000000 -r 65ce27f0fa01 test-data/sample.db Binary file test-data/sample.db has changed diff -r 000000000000 -r 65ce27f0fa01 test-data/sample.mzlite Binary file test-data/sample.mzlite has changed diff -r 000000000000 -r 65ce27f0fa01 test-data/sample.qpsm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.qpsm Fri Sep 10 05:41:32 2021 +0000 @@ -0,0 +1,4 @@ +PSMId GlobalMod PepSequenceID ModSequenceID Label ScanNr ScanTime Charge PrecursorMZ TheoMass AbsDeltaMass PeptideLength MissCleavages SequestScore SequestNormDeltaBestToRest SequestNormDeltaNext AndroScore AndroNormDeltaBestToRest AndroNormDeltaNext XtandemScore XtandemNormDeltaBestToRest XtandemNormDeltaNext ModelScore QValue PEPValue StringSequence ProteinNames +sample=0 period=1 cycle=2033 experiment=4 1 4 8 1 0 32.9949 2 383.2268582 764.4508194 0.01165603632 7 0 8.635639049 0 0.6779896705 112.3264921 0 0.7657267969 45.72186797 0 0.5594493789 NaN NaN NaN ILVGDIK Cre02.g143307.t1.1 +sample=0 period=1 cycle=2043 experiment=5 0 22 87 1 2 33.36088333 2 399.242789 796.4806883 0.009663316474 7 0 7.816376209 0 0.8192994029 74.99645487 0 1 29.37298389 0 0.7506817907 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1 +sample=0 period=1 cycle=2038 experiment=7 1 22 88 1 1 33.18005 2 404.2288055 806.4510372 0.007979227388 7 0 7.830779576 0 0.7970537368 112.937008 0 0.8973792939 47.98049859 0 0.6070363597 NaN NaN NaN ALEVIPR Cre01.g026550.t1.1