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comparison macros.xml @ 3:2d67fb758956 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 11:50:09 -0400
parents 256cc0e17454
children 9cb7dcc07dae
comparison
equal deleted inserted replaced
2:3fc2116ac6d9 3:2d67fb758956
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">1.6.3.4</token> 3 <token name="@VERSION@">1.6.10.43</token>
4 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> 4 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
5 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 5 <token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
6 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> 6 - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]
7 <filter>'@NAME@' in output</filter> 7 - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]
8 </data> 8 - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]
9 </xml> 9 - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True]
10 <xml name="output_option" token_label="default label" token_name="default"> 10 - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True]
11 <option value="@NAME@">@LABEL@</option> 11 - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True]
12 - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]
13 - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]
14 - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]
15 ]]></token>
16
17 <xml name="requirements">
18 <requirements>
19 <requirement type="package" version="@VERSION@">maxquant</requirement>
20 <requirement type="package" version="3.7">python</requirement>
21 <requirement type="package" version="5.1.2">pyyaml</requirement>
22 <requirement type="package" version="0.92.6">r-ptxqc</requirement>
23 <requirement type="package" version="1.32">tar</requirement>
24 </requirements>
25 </xml>
26
27 <xml name="ptxqc">
28 <configfile name="qr_yaml">
29 PTXQC:
30 ReportFilename:
31 extended: yes
32 UseLocalMQPar: yes
33 NameLengthMax_num: 10.0
34 OutputFormats:
35 - plainPDF
36 PlainPDF:
37 AddPageNumbers: 'on'
38 File:
39 Parameters:
40 #if $qc.do_it:
41 enabled: ${qc.parameters}
42 #end if
43 Summary:
44 #if $qc.do_it:
45 enabled: ${qc.summary}
46 #end if
47 IDRate:
48 Thresh_bad_num: 20.0
49 Thresh_great_num: 35.0
50 ProteinGroups:
51 #if $qc.do_it:
52 enabled: ${qc.proteingroups}
53 #end if
54 RatioPlot:
55 LabelIncThresh_num: 4.0
56 IntensityThreshLog2_num: 25.0
57 Evidence:
58 #if $qc.do_it:
59 enabled: ${qc.evidence}
60 #end if
61 ProteinCountThresh_num: 3500.0
62 IntensityThreshLog2_num: 23.0
63 PeptideCountThresh_num: 15000.0
64 SpecialContaminants:
65 cont_MYCO:
66 - MYCOPLASMA
67 - '1'
68 MQpar_MatchingTimeWindow_num: 0.0
69 MatchBetweenRuns_wA: auto
70 MQpar_firstSearchTol_num: 20.0
71 firstSearch_outOfCalWarnSD_num: 2.0
72 MQpar_mainSearchTol_num: 4.5
73 MsMs:
74 #if $qc.do_it:
75 enabled: ${qc.msms}
76 #end if
77 MsMsScans:
78 #if $qc.do_it:
79 enabled: ${qc.msmsscans}
80 #end if
81 IonInjectionThresh_num: 10.0
82 order:
83 qcMetric_PAR: 1.0
84 qcMetric_PG_PCA: 3.0
85 qcMetric_EVD_Top5Cont: 10.0
86 qcMetric_PG_Ratio: 19.0
87 qcMetric_EVD_UserContaminant: 20.0
88 qcMetric_EVD_PeptideInt: 30.0
89 qcMetric_EVD_ReporterInt: 31.0
90 qcMetric_PG_RawInt: 32.0
91 qcMetric_PG_LFQInt: 33.0
92 qcMetric_PG_ReporterInt: 34.0
93 qcMetric_MSMS_MissedCleavages: 40.0
94 qcMetric_EVD_Charge: 100.0
95 qcMetric_PG_Cont: 110.0
96 qcMetric_MSMSScans_TopNoverRT: 120.0
97 qcMetric_EVD_IDoverRT: 150.0
98 qcMetric_EVD_RTPeakWidth: 170.0
99 qcMetric_EVD_MBRAlign: 210.0
100 qcMetric_EVD_MBRIdTransfer: 220.0
101 qcMetric_EVD_MBRaux: 221.0
102 qcMetric_MSMSScans_IonInjTime: 240.0
103 qcMetric_MSMSScans_MSMSIntensity: 245.0
104 qcMetric_EVD_MS2OverSampling: 250.0
105 qcMetric_EVD_PreCal: 260.0
106 qcMetric_EVD_PostCal: 270.0
107 qcMetric_MSMS_MSMSDecal: 280.0
108 qcMetric_SM_MSMSIdRate: 300.0
109 qcMetric_MSMSScans_TopNID: 380.0
110 qcMetric_MSMSScans_DepPep: 383.0
111 qcMetric_EVD_MissingValues: 390.0
112 qcMetric_EVD_PeptideCount: 400.0
113 qcMetric_EVD_ProteinCount: 450.0
114 qcMetric_AverageQualOverall: 9999.0
115 </configfile>
116 <configfile name="qr">
117 library(PTXQC)
118 library(yaml)
119 library(methods)
120 args = commandArgs(trailingOnly=TRUE)
121 yaml_config = yaml.load_file(input = args[1])
122 r = createReport('./combined/txt', yaml_config)
123 cat(paste0("\nReport generated as '", r\$report_file, "'\n\n"))
124 </configfile>
125 </xml>
126
127 <xml name="mod_option" token_value="default">
128 <option value="@VALUE@">@VALUE@</option>
129 </xml>
130 <xml name="default_mod_option" token_value="default">
131 <option selected="true" value="@VALUE@">@VALUE@</option>
132 </xml>
133
134 <xml name="ptxqc-opts">
135 <conditional name="qc">
136 <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (at own risk)"
137 type="boolean" checked="false"/>
138 <when value="true">
139 <param name="parameters" type="boolean" checked="true"
140 label="use parameters.txt?" truevalue="yes" falsevalue="no" />
141 <param name="summary" type="boolean" checked="true"
142 label="use summary.txt?" truevalue="yes" falsevalue="no" />
143 <param name="proteingroups" type="boolean" checked="true"
144 label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" />
145 <param name="evidence" type="boolean" checked="true"
146 label="use evidence.txt?" truevalue="yes" falsevalue="no" />
147 <param name="msms" type="boolean" checked="true"
148 label="use msms.txt?" truevalue="yes" falsevalue="no" />
149 <param name="msmsscans" type="boolean" checked="true"
150 label="use msmsScans.txt?" truevalue="yes" falsevalue="no" />
151 </when>
152 <when value="false"/>
153 </conditional>
154 </xml>
155
156 <xml name="outputs">
157 <outputs>
158 <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>
159 <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/>
160 <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/>
161 <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/>
162 <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/>
163 <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/>
164 <expand macro="output_from_wdir" name="mzTab" label="mzTab" ext="mzTab"/>
165 <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/>
166 <expand macro="output_from_wdir" name="libraryMatch" label="library match"/>
167 <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/>
168 <expand macro="output_from_wdir" name="modificationSpecificPeptides" label="modification specific peptides"/>
169 <expand macro="output_from_wdir" name="ms3Scans" label="ms3 scans"/>
170 <expand macro="output_from_wdir" name="msmsScans" label="msms Scans"/>
171 <expand macro="output_from_wdir" name="mzRange" label="mz range"/>
172 <expand macro="output_from_wdir" name="peptideSection" label="peptide section"/>
173 <expand macro="output_from_wdir" name="summary" label="MaxQuant summary"/>
174 <expand macro="output" name="output_all" format="tar" label="'combined/txt/' directory"/>
175 <expand macro="output" name="log" format="txt" label="log"/>
176 <expand macro="output" name="config" format="txt" label="yaml config file"/>
177 <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">
178 <filter>qc['do_it'] == True</filter>
179 </data>
180 </outputs>
181 </xml>
182
183 <xml name="modification">
184 <expand macro="mod_option" value="Acetyl (K)"/>
185 <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
186 <expand macro="mod_option" value="Carbamidomethyl (C)"/>
187 <expand macro="mod_option" value="Oxidation (M)"/>
188 <expand macro="mod_option" value="Phospho (STY)"/>
189 <expand macro="mod_option" value="GlyGly (K)"/>
190 <expand macro="mod_option" value="Methyl (KR)"/>
191 <expand macro="mod_option" value="Dimethyl (KR)"/>
192 <expand macro="mod_option" value="Trimethyl (K)"/>
193 <expand macro="mod_option" value="Pro5"/>
194 <expand macro="mod_option" value="Pro6"/>
195 <expand macro="mod_option" value="Glu-&gt;pyro-Glu"/>
196 <expand macro="mod_option" value="Gln-&gt;pyro-Glu"/>
197 <expand macro="mod_option" value="QQTGG (K)"/>
198 <expand macro="mod_option" value="Deamidation (N)"/>
199 <expand macro="mod_option" value="Deamidation 18O (N)"/>
200 <expand macro="mod_option" value="Deamidation (NQ)"/>
201 <expand macro="mod_option" value="Hydroxyproline"/>
202 <expand macro="mod_option" value="Carbamyl (N-term)"/>
203 <expand macro="mod_option" value="Delta:H(2)C(2) (N-term)"/>
204 <expand macro="mod_option" value="Dioxidation (MW)"/>
205 <expand macro="mod_option" value="Trioxidation (C)"/>
206 <expand macro="mod_option" value="Dethiomethyl (M)"/>
207 <expand macro="mod_option" value="Cation:Na (DE)"/>
208 <expand macro="mod_option" value="Methyl (E)"/>
209 <expand macro="mod_option" value="Dehydrated (ST)"/>
210 <expand macro="mod_option" value="Oxidation (P)"/>
211 <expand macro="mod_option" value="Dimethyl (K)"/>
212 <expand macro="mod_option" value="Amidated (Protein C-term)"/>
213 <expand macro="mod_option" value="Sulfo (STY)"/>
214 <expand macro="mod_option" value="Acetyl (N-term)"/>
215 <expand macro="mod_option" value="Amidated (C-term)"/>
216 <expand macro="mod_option" value="Sulfation (Y)"/>
217 <expand macro="mod_option" value="Phospho (ST)"/>
218 <expand macro="mod_option" value="Cys-Cys"/>
219 <expand macro="mod_option" value="Ala-&gt;Arg"/>
220 <expand macro="mod_option" value="Ala-&gt;Asn"/>
221 <expand macro="mod_option" value="Ala-&gt;Asp"/>
222 <expand macro="mod_option" value="Ala-&gt;Cys"/>
223 <expand macro="mod_option" value="Ala-&gt;Gln"/>
224 <expand macro="mod_option" value="Ala-&gt;Glu"/>
225 <expand macro="mod_option" value="Ala-&gt;Gly"/>
226 <expand macro="mod_option" value="Ala-&gt;His"/>
227 <expand macro="mod_option" value="Ala-&gt;Xle"/>
228 <expand macro="mod_option" value="Ala-&gt;Lys"/>
229 <expand macro="mod_option" value="Ala-&gt;Met"/>
230 <expand macro="mod_option" value="Ala-&gt;Phe"/>
231 <expand macro="mod_option" value="Ala-&gt;Pro"/>
232 <expand macro="mod_option" value="Ala-&gt;Ser"/>
233 <expand macro="mod_option" value="Ala-&gt;Thr"/>
234 <expand macro="mod_option" value="Ala-&gt;Trp"/>
235 <expand macro="mod_option" value="Ala-&gt;Tyr"/>
236 <expand macro="mod_option" value="Ala-&gt;Val"/>
237 <expand macro="mod_option" value="Arg-&gt;Ala"/>
238 <expand macro="mod_option" value="Arg-&gt;Asn"/>
239 <expand macro="mod_option" value="Arg-&gt;Asp"/>
240 <expand macro="mod_option" value="Arg-&gt;Cys"/>
241 <expand macro="mod_option" value="Arg-&gt;Gln"/>
242 <expand macro="mod_option" value="Arg-&gt;Glu"/>
243 <expand macro="mod_option" value="Arg-&gt;Gly"/>
244 <expand macro="mod_option" value="Arg-&gt;His"/>
245 <expand macro="mod_option" value="Arg-&gt;Lys"/>
246 <expand macro="mod_option" value="Arg-&gt;Met"/>
247 <expand macro="mod_option" value="Arg-&gt;Phe"/>
248 <expand macro="mod_option" value="Arg-&gt;Pro"/>
249 <expand macro="mod_option" value="Arg-&gt;Ser"/>
250 <expand macro="mod_option" value="Arg-&gt;Thr"/>
251 <expand macro="mod_option" value="Arg-&gt;Trp"/>
252 <expand macro="mod_option" value="Arg-&gt;Tyr"/>
253 <expand macro="mod_option" value="Arg-&gt;Val"/>
254 <expand macro="mod_option" value="Arg-&gt;Xle"/>
255 <expand macro="mod_option" value="Asn-&gt;Ala"/>
256 <expand macro="mod_option" value="Asn-&gt;Arg"/>
257 <expand macro="mod_option" value="Asn-&gt;Asp"/>
258 <expand macro="mod_option" value="Asn-&gt;Cys"/>
259 <expand macro="mod_option" value="Asn-&gt;Gln"/>
260 <expand macro="mod_option" value="Asn-&gt;Glu"/>
261 <expand macro="mod_option" value="Asn-&gt;Gly"/>
262 <expand macro="mod_option" value="Asn-&gt;His"/>
263 <expand macro="mod_option" value="Asn-&gt;Lys"/>
264 <expand macro="mod_option" value="Asn-&gt;Met"/>
265 <expand macro="mod_option" value="Asn-&gt;Phe"/>
266 <expand macro="mod_option" value="Asn-&gt;Pro"/>
267 <expand macro="mod_option" value="Asn-&gt;Ser"/>
268 <expand macro="mod_option" value="Asn-&gt;Thr"/>
269 <expand macro="mod_option" value="Asn-&gt;Trp"/>
270 <expand macro="mod_option" value="Asn-&gt;Tyr"/>
271 <expand macro="mod_option" value="Asn-&gt;Val"/>
272 <expand macro="mod_option" value="Asn-&gt;Xle"/>
273 <expand macro="mod_option" value="Asp-&gt;Ala"/>
274 <expand macro="mod_option" value="Asp-&gt;Arg"/>
275 <expand macro="mod_option" value="Asp-&gt;Asn"/>
276 <expand macro="mod_option" value="Asp-&gt;Cys"/>
277 <expand macro="mod_option" value="Asp-&gt;Gln"/>
278 <expand macro="mod_option" value="Asp-&gt;Glu"/>
279 <expand macro="mod_option" value="Asp-&gt;Gly"/>
280 <expand macro="mod_option" value="Asp-&gt;His"/>
281 <expand macro="mod_option" value="Asp-&gt;Lys"/>
282 <expand macro="mod_option" value="Asp-&gt;Met"/>
283 <expand macro="mod_option" value="Asp-&gt;Phe"/>
284 <expand macro="mod_option" value="Asp-&gt;Pro"/>
285 <expand macro="mod_option" value="Asp-&gt;Ser"/>
286 <expand macro="mod_option" value="Asp-&gt;Thr"/>
287 <expand macro="mod_option" value="Asp-&gt;Trp"/>
288 <expand macro="mod_option" value="Asp-&gt;Tyr"/>
289 <expand macro="mod_option" value="Asp-&gt;Val"/>
290 <expand macro="mod_option" value="Asp-&gt;Xle"/>
291 <expand macro="mod_option" value="Cys-&gt;Ala"/>
292 <expand macro="mod_option" value="Cys-&gt;Arg"/>
293 <expand macro="mod_option" value="Cys-&gt;Asn"/>
294 <expand macro="mod_option" value="Cys-&gt;Asp"/>
295 <expand macro="mod_option" value="Cys-&gt;Gln"/>
296 <expand macro="mod_option" value="Cys-&gt;Glu"/>
297 <expand macro="mod_option" value="Cys-&gt;Gly"/>
298 <expand macro="mod_option" value="Cys-&gt;His"/>
299 <expand macro="mod_option" value="Cys-&gt;Lys"/>
300 <expand macro="mod_option" value="Cys-&gt;Met"/>
301 <expand macro="mod_option" value="Cys-&gt;Phe"/>
302 <expand macro="mod_option" value="Cys-&gt;Pro"/>
303 <expand macro="mod_option" value="Cys-&gt;Ser"/>
304 <expand macro="mod_option" value="Cys-&gt;Thr"/>
305 <expand macro="mod_option" value="Cys-&gt;Trp"/>
306 <expand macro="mod_option" value="Cys-&gt;Tyr"/>
307 <expand macro="mod_option" value="Cys-&gt;Val"/>
308 <expand macro="mod_option" value="Cys-&gt;Xle"/>
309 <expand macro="mod_option" value="Gln-&gt;Ala"/>
310 <expand macro="mod_option" value="Gln-&gt;Arg"/>
311 <expand macro="mod_option" value="Gln-&gt;Asn"/>
312 <expand macro="mod_option" value="Gln-&gt;Asp"/>
313 <expand macro="mod_option" value="Gln-&gt;Cys"/>
314 <expand macro="mod_option" value="Gln-&gt;Glu"/>
315 <expand macro="mod_option" value="Gln-&gt;Gly"/>
316 <expand macro="mod_option" value="Gln-&gt;His"/>
317 <expand macro="mod_option" value="Gln-&gt;Lys"/>
318 <expand macro="mod_option" value="Gln-&gt;Met"/>
319 <expand macro="mod_option" value="Gln-&gt;Phe"/>
320 <expand macro="mod_option" value="Gln-&gt;Pro"/>
321 <expand macro="mod_option" value="Gln-&gt;Ser"/>
322 <expand macro="mod_option" value="Gln-&gt;Thr"/>
323 <expand macro="mod_option" value="Gln-&gt;Trp"/>
324 <expand macro="mod_option" value="Gln-&gt;Tyr"/>
325 <expand macro="mod_option" value="Gln-&gt;Val"/>
326 <expand macro="mod_option" value="Gln-&gt;Xle"/>
327 <expand macro="mod_option" value="Glu-&gt;Ala"/>
328 <expand macro="mod_option" value="Glu-&gt;Arg"/>
329 <expand macro="mod_option" value="Glu-&gt;Asn"/>
330 <expand macro="mod_option" value="Glu-&gt;Asp"/>
331 <expand macro="mod_option" value="Glu-&gt;Cys"/>
332 <expand macro="mod_option" value="Glu-&gt;Gln"/>
333 <expand macro="mod_option" value="Glu-&gt;Gly"/>
334 <expand macro="mod_option" value="Glu-&gt;His"/>
335 <expand macro="mod_option" value="Glu-&gt;Lys"/>
336 <expand macro="mod_option" value="Glu-&gt;Met"/>
337 <expand macro="mod_option" value="Glu-&gt;Phe"/>
338 <expand macro="mod_option" value="Glu-&gt;Pro"/>
339 <expand macro="mod_option" value="Glu-&gt;Ser"/>
340 <expand macro="mod_option" value="Glu-&gt;Thr"/>
341 <expand macro="mod_option" value="Glu-&gt;Trp"/>
342 <expand macro="mod_option" value="Glu-&gt;Tyr"/>
343 <expand macro="mod_option" value="Glu-&gt;Val"/>
344 <expand macro="mod_option" value="Glu-&gt;Xle"/>
345 <expand macro="mod_option" value="Gly-&gt;Ala"/>
346 <expand macro="mod_option" value="Gly-&gt;Arg"/>
347 <expand macro="mod_option" value="Gly-&gt;Asn"/>
348 <expand macro="mod_option" value="Gly-&gt;Asp"/>
349 <expand macro="mod_option" value="Gly-&gt;Cys"/>
350 <expand macro="mod_option" value="Gly-&gt;Gln"/>
351 <expand macro="mod_option" value="Gly-&gt;Glu"/>
352 <expand macro="mod_option" value="Gly-&gt;His"/>
353 <expand macro="mod_option" value="Gly-&gt;Lys"/>
354 <expand macro="mod_option" value="Gly-&gt;Met"/>
355 <expand macro="mod_option" value="Gly-&gt;Phe"/>
356 <expand macro="mod_option" value="Gly-&gt;Pro"/>
357 <expand macro="mod_option" value="Gly-&gt;Ser"/>
358 <expand macro="mod_option" value="Gly-&gt;Thr"/>
359 <expand macro="mod_option" value="Gly-&gt;Trp"/>
360 <expand macro="mod_option" value="Gly-&gt;Tyr"/>
361 <expand macro="mod_option" value="Gly-&gt;Val"/>
362 <expand macro="mod_option" value="Gly-&gt;Xle"/>
363 <expand macro="mod_option" value="His-&gt;Ala"/>
364 <expand macro="mod_option" value="His-&gt;Arg"/>
365 <expand macro="mod_option" value="His-&gt;Asn"/>
366 <expand macro="mod_option" value="His-&gt;Asp"/>
367 <expand macro="mod_option" value="His-&gt;Cys"/>
368 <expand macro="mod_option" value="His-&gt;Gln"/>
369 <expand macro="mod_option" value="His-&gt;Glu"/>
370 <expand macro="mod_option" value="His-&gt;Gly"/>
371 <expand macro="mod_option" value="His-&gt;Lys"/>
372 <expand macro="mod_option" value="His-&gt;Met"/>
373 <expand macro="mod_option" value="His-&gt;Phe"/>
374 <expand macro="mod_option" value="His-&gt;Pro"/>
375 <expand macro="mod_option" value="His-&gt;Ser"/>
376 <expand macro="mod_option" value="His-&gt;Thr"/>
377 <expand macro="mod_option" value="His-&gt;Trp"/>
378 <expand macro="mod_option" value="His-&gt;Tyr"/>
379 <expand macro="mod_option" value="His-&gt;Val"/>
380 <expand macro="mod_option" value="His-&gt;Xle"/>
381 <expand macro="mod_option" value="Lys-&gt;Ala"/>
382 <expand macro="mod_option" value="Lys-&gt;Arg"/>
383 <expand macro="mod_option" value="Lys-&gt;Asn"/>
384 <expand macro="mod_option" value="Lys-&gt;Asp"/>
385 <expand macro="mod_option" value="Lys-&gt;Cys"/>
386 <expand macro="mod_option" value="Lys-&gt;Gln"/>
387 <expand macro="mod_option" value="Lys-&gt;Glu"/>
388 <expand macro="mod_option" value="Lys-&gt;Gly"/>
389 <expand macro="mod_option" value="Lys-&gt;His"/>
390 <expand macro="mod_option" value="Lys-&gt;Met"/>
391 <expand macro="mod_option" value="Lys-&gt;Phe"/>
392 <expand macro="mod_option" value="Lys-&gt;Pro"/>
393 <expand macro="mod_option" value="Lys-&gt;Ser"/>
394 <expand macro="mod_option" value="Lys-&gt;Thr"/>
395 <expand macro="mod_option" value="Lys-&gt;Trp"/>
396 <expand macro="mod_option" value="Lys-&gt;Tyr"/>
397 <expand macro="mod_option" value="Lys-&gt;Val"/>
398 <expand macro="mod_option" value="Lys-&gt;Xle"/>
399 <expand macro="mod_option" value="Met-&gt;Ala"/>
400 <expand macro="mod_option" value="Met-&gt;Arg"/>
401 <expand macro="mod_option" value="Met-&gt;Asn"/>
402 <expand macro="mod_option" value="Met-&gt;Asp"/>
403 <expand macro="mod_option" value="Met-&gt;Cys"/>
404 <expand macro="mod_option" value="Met-&gt;Gln"/>
405 <expand macro="mod_option" value="Met-&gt;Glu"/>
406 <expand macro="mod_option" value="Met-&gt;Gly"/>
407 <expand macro="mod_option" value="Met-&gt;His"/>
408 <expand macro="mod_option" value="Met-&gt;Lys"/>
409 <expand macro="mod_option" value="Met-&gt;Phe"/>
410 <expand macro="mod_option" value="Met-&gt;Pro"/>
411 <expand macro="mod_option" value="Met-&gt;Ser"/>
412 <expand macro="mod_option" value="Met-&gt;Thr"/>
413 <expand macro="mod_option" value="Met-&gt;Trp"/>
414 <expand macro="mod_option" value="Met-&gt;Tyr"/>
415 <expand macro="mod_option" value="Met-&gt;Val"/>
416 <expand macro="mod_option" value="Met-&gt;Xle"/>
417 <expand macro="mod_option" value="Phe-&gt;Ala"/>
418 <expand macro="mod_option" value="Phe-&gt;Arg"/>
419 <expand macro="mod_option" value="Phe-&gt;Asn"/>
420 <expand macro="mod_option" value="Phe-&gt;Asp"/>
421 <expand macro="mod_option" value="Phe-&gt;Cys"/>
422 <expand macro="mod_option" value="Phe-&gt;Gln"/>
423 <expand macro="mod_option" value="Phe-&gt;Glu"/>
424 <expand macro="mod_option" value="Phe-&gt;Gly"/>
425 <expand macro="mod_option" value="Phe-&gt;His"/>
426 <expand macro="mod_option" value="Phe-&gt;Lys"/>
427 <expand macro="mod_option" value="Phe-&gt;Met"/>
428 <expand macro="mod_option" value="Phe-&gt;Pro"/>
429 <expand macro="mod_option" value="Phe-&gt;Ser"/>
430 <expand macro="mod_option" value="Phe-&gt;Thr"/>
431 <expand macro="mod_option" value="Phe-&gt;Trp"/>
432 <expand macro="mod_option" value="Phe-&gt;Tyr"/>
433 <expand macro="mod_option" value="Phe-&gt;Val"/>
434 <expand macro="mod_option" value="Phe-&gt;Xle"/>
435 <expand macro="mod_option" value="Pro-&gt;Ala"/>
436 <expand macro="mod_option" value="Pro-&gt;Arg"/>
437 <expand macro="mod_option" value="Pro-&gt;Asn"/>
438 <expand macro="mod_option" value="Pro-&gt;Asp"/>
439 <expand macro="mod_option" value="Pro-&gt;Cys"/>
440 <expand macro="mod_option" value="Pro-&gt;Gln"/>
441 <expand macro="mod_option" value="Pro-&gt;Glu"/>
442 <expand macro="mod_option" value="Pro-&gt;Gly"/>
443 <expand macro="mod_option" value="Pro-&gt;His"/>
444 <expand macro="mod_option" value="Pro-&gt;Lys"/>
445 <expand macro="mod_option" value="Pro-&gt;Met"/>
446 <expand macro="mod_option" value="Pro-&gt;Phe"/>
447 <expand macro="mod_option" value="Pro-&gt;Ser"/>
448 <expand macro="mod_option" value="Pro-&gt;Thr"/>
449 <expand macro="mod_option" value="Pro-&gt;Trp"/>
450 <expand macro="mod_option" value="Pro-&gt;Tyr"/>
451 <expand macro="mod_option" value="Pro-&gt;Val"/>
452 <expand macro="mod_option" value="Pro-&gt;Xle"/>
453 <expand macro="mod_option" value="Ser-&gt;Ala"/>
454 <expand macro="mod_option" value="Ser-&gt;Arg"/>
455 <expand macro="mod_option" value="Ser-&gt;Asn"/>
456 <expand macro="mod_option" value="Ser-&gt;Asp"/>
457 <expand macro="mod_option" value="Ser-&gt;Cys"/>
458 <expand macro="mod_option" value="Ser-&gt;Gln"/>
459 <expand macro="mod_option" value="Ser-&gt;Glu"/>
460 <expand macro="mod_option" value="Ser-&gt;Gly"/>
461 <expand macro="mod_option" value="Ser-&gt;His"/>
462 <expand macro="mod_option" value="Ser-&gt;Lys"/>
463 <expand macro="mod_option" value="Ser-&gt;Met"/>
464 <expand macro="mod_option" value="Ser-&gt;Phe"/>
465 <expand macro="mod_option" value="Ser-&gt;Pro"/>
466 <expand macro="mod_option" value="Ser-&gt;Thr"/>
467 <expand macro="mod_option" value="Ser-&gt;Trp"/>
468 <expand macro="mod_option" value="Ser-&gt;Tyr"/>
469 <expand macro="mod_option" value="Ser-&gt;Val"/>
470 <expand macro="mod_option" value="Ser-&gt;Xle"/>
471 <expand macro="mod_option" value="Thr-&gt;Ala"/>
472 <expand macro="mod_option" value="Thr-&gt;Arg"/>
473 <expand macro="mod_option" value="Thr-&gt;Asn"/>
474 <expand macro="mod_option" value="Thr-&gt;Asp"/>
475 <expand macro="mod_option" value="Thr-&gt;Cys"/>
476 <expand macro="mod_option" value="Thr-&gt;Gln"/>
477 <expand macro="mod_option" value="Thr-&gt;Glu"/>
478 <expand macro="mod_option" value="Thr-&gt;Gly"/>
479 <expand macro="mod_option" value="Thr-&gt;His"/>
480 <expand macro="mod_option" value="Thr-&gt;Lys"/>
481 <expand macro="mod_option" value="Thr-&gt;Met"/>
482 <expand macro="mod_option" value="Thr-&gt;Phe"/>
483 <expand macro="mod_option" value="Thr-&gt;Pro"/>
484 <expand macro="mod_option" value="Thr-&gt;Ser"/>
485 <expand macro="mod_option" value="Thr-&gt;Trp"/>
486 <expand macro="mod_option" value="Thr-&gt;Tyr"/>
487 <expand macro="mod_option" value="Thr-&gt;Val"/>
488 <expand macro="mod_option" value="Thr-&gt;Xle"/>
489 <expand macro="mod_option" value="Trp-&gt;Ala"/>
490 <expand macro="mod_option" value="Trp-&gt;Arg"/>
491 <expand macro="mod_option" value="Trp-&gt;Asn"/>
492 <expand macro="mod_option" value="Trp-&gt;Asp"/>
493 <expand macro="mod_option" value="Trp-&gt;Cys"/>
494 <expand macro="mod_option" value="Trp-&gt;Gln"/>
495 <expand macro="mod_option" value="Trp-&gt;Glu"/>
496 <expand macro="mod_option" value="Trp-&gt;Gly"/>
497 <expand macro="mod_option" value="Trp-&gt;His"/>
498 <expand macro="mod_option" value="Trp-&gt;Lys"/>
499 <expand macro="mod_option" value="Trp-&gt;Met"/>
500 <expand macro="mod_option" value="Trp-&gt;Phe"/>
501 <expand macro="mod_option" value="Trp-&gt;Pro"/>
502 <expand macro="mod_option" value="Trp-&gt;Ser"/>
503 <expand macro="mod_option" value="Trp-&gt;Thr"/>
504 <expand macro="mod_option" value="Trp-&gt;Tyr"/>
505 <expand macro="mod_option" value="Trp-&gt;Val"/>
506 <expand macro="mod_option" value="Trp-&gt;Xle"/>
507 <expand macro="mod_option" value="Tyr-&gt;Ala"/>
508 <expand macro="mod_option" value="Tyr-&gt;Arg"/>
509 <expand macro="mod_option" value="Tyr-&gt;Asn"/>
510 <expand macro="mod_option" value="Tyr-&gt;Asp"/>
511 <expand macro="mod_option" value="Tyr-&gt;Cys"/>
512 <expand macro="mod_option" value="Tyr-&gt;Gln"/>
513 <expand macro="mod_option" value="Tyr-&gt;Glu"/>
514 <expand macro="mod_option" value="Tyr-&gt;Gly"/>
515 <expand macro="mod_option" value="Tyr-&gt;His"/>
516 <expand macro="mod_option" value="Tyr-&gt;Lys"/>
517 <expand macro="mod_option" value="Tyr-&gt;Met"/>
518 <expand macro="mod_option" value="Tyr-&gt;Phe"/>
519 <expand macro="mod_option" value="Tyr-&gt;Pro"/>
520 <expand macro="mod_option" value="Tyr-&gt;Ser"/>
521 <expand macro="mod_option" value="Tyr-&gt;Thr"/>
522 <expand macro="mod_option" value="Tyr-&gt;Trp"/>
523 <expand macro="mod_option" value="Tyr-&gt;Val"/>
524 <expand macro="mod_option" value="Tyr-&gt;Xle"/>
525 <expand macro="mod_option" value="Val-&gt;Ala"/>
526 <expand macro="mod_option" value="Val-&gt;Arg"/>
527 <expand macro="mod_option" value="Val-&gt;Asn"/>
528 <expand macro="mod_option" value="Val-&gt;Asp"/>
529 <expand macro="mod_option" value="Val-&gt;Cys"/>
530 <expand macro="mod_option" value="Val-&gt;Gln"/>
531 <expand macro="mod_option" value="Val-&gt;Glu"/>
532 <expand macro="mod_option" value="Val-&gt;Gly"/>
533 <expand macro="mod_option" value="Val-&gt;His"/>
534 <expand macro="mod_option" value="Val-&gt;Lys"/>
535 <expand macro="mod_option" value="Val-&gt;Met"/>
536 <expand macro="mod_option" value="Val-&gt;Phe"/>
537 <expand macro="mod_option" value="Val-&gt;Pro"/>
538 <expand macro="mod_option" value="Val-&gt;Ser"/>
539 <expand macro="mod_option" value="Val-&gt;Thr"/>
540 <expand macro="mod_option" value="Val-&gt;Trp"/>
541 <expand macro="mod_option" value="Val-&gt;Tyr"/>
542 <expand macro="mod_option" value="Val-&gt;Xle"/>
543 <expand macro="mod_option" value="Xle-&gt;Ala"/>
544 <expand macro="mod_option" value="Xle-&gt;Arg"/>
545 <expand macro="mod_option" value="Xle-&gt;Asn"/>
546 <expand macro="mod_option" value="Xle-&gt;Asp"/>
547 <expand macro="mod_option" value="Xle-&gt;Cys"/>
548 <expand macro="mod_option" value="Xle-&gt;Gln"/>
549 <expand macro="mod_option" value="Xle-&gt;Glu"/>
550 <expand macro="mod_option" value="Xle-&gt;Gly"/>
551 <expand macro="mod_option" value="Xle-&gt;His"/>
552 <expand macro="mod_option" value="Xle-&gt;Lys"/>
553 <expand macro="mod_option" value="Xle-&gt;Met"/>
554 <expand macro="mod_option" value="Xle-&gt;Phe"/>
555 <expand macro="mod_option" value="Xle-&gt;Pro"/>
556 <expand macro="mod_option" value="Xle-&gt;Ser"/>
557 <expand macro="mod_option" value="Xle-&gt;Thr"/>
558 <expand macro="mod_option" value="Xle-&gt;Trp"/>
559 <expand macro="mod_option" value="Xle-&gt;Tyr"/>
560 <expand macro="mod_option" value="Xle-&gt;Val"/>
561 <expand macro="mod_option" value="CamCys-&gt;Ala"/>
562 <expand macro="mod_option" value="CamCys-&gt;Arg"/>
563 <expand macro="mod_option" value="CamCys-&gt;Asn"/>
564 <expand macro="mod_option" value="CamCys-&gt;Asp"/>
565 <expand macro="mod_option" value="CamCys-&gt;Gln"/>
566 <expand macro="mod_option" value="CamCys-&gt;Glu"/>
567 <expand macro="mod_option" value="CamCys-&gt;Gly"/>
568 <expand macro="mod_option" value="CamCys-&gt;His"/>
569 <expand macro="mod_option" value="CamCys-&gt;Lys"/>
570 <expand macro="mod_option" value="CamCys-&gt;Met"/>
571 <expand macro="mod_option" value="CamCys-&gt;Phe"/>
572 <expand macro="mod_option" value="CamCys-&gt;Pro"/>
573 <expand macro="mod_option" value="CamCys-&gt;Ser"/>
574 <expand macro="mod_option" value="CamCys-&gt;Thr"/>
575 <expand macro="mod_option" value="CamCys-&gt;Trp"/>
576 <expand macro="mod_option" value="CamCys-&gt;Tyr"/>
577 <expand macro="mod_option" value="CamCys-&gt;Val"/>
578 <expand macro="mod_option" value="CamCys-&gt;Xle"/>
579 <expand macro="mod_option" value="Ala-&gt;CamCys"/>
580 <expand macro="mod_option" value="Arg-&gt;CamCys"/>
581 <expand macro="mod_option" value="Asn-&gt;CamCys"/>
582 <expand macro="mod_option" value="Asp-&gt;CamCys"/>
583 <expand macro="mod_option" value="Gln-&gt;CamCys"/>
584 <expand macro="mod_option" value="Glu-&gt;CamCys"/>
585 <expand macro="mod_option" value="Gly-&gt;CamCys"/>
586 <expand macro="mod_option" value="His-&gt;CamCys"/>
587 <expand macro="mod_option" value="Lys-&gt;CamCys"/>
588 <expand macro="mod_option" value="Met-&gt;CamCys"/>
589 <expand macro="mod_option" value="Phe-&gt;CamCys"/>
590 <expand macro="mod_option" value="Pro-&gt;CamCys"/>
591 <expand macro="mod_option" value="Ser-&gt;CamCys"/>
592 <expand macro="mod_option" value="Thr-&gt;CamCys"/>
593 <expand macro="mod_option" value="Trp-&gt;CamCys"/>
594 <expand macro="mod_option" value="Tyr-&gt;CamCys"/>
595 <expand macro="mod_option" value="Val-&gt;CamCys"/>
596 <expand macro="mod_option" value="Xle-&gt;CamCys"/>
597 <expand macro="mod_option" value="Cysteinyl"/>
598 <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/>
599 </xml>
600
601 <xml name="label">
602 <expand macro="mod_option" value="Arg6"/>
603 <expand macro="mod_option" value="Arg10"/>
604 <expand macro="mod_option" value="Lys4"/>
605 <expand macro="mod_option" value="Lys6"/>
606 <expand macro="mod_option" value="Lys8"/>
607 <expand macro="mod_option" value="DimethLys0"/>
608 <expand macro="mod_option" value="DimethNter0"/>
609 <expand macro="mod_option" value="DimethLys4"/>
610 <expand macro="mod_option" value="DimethNter4"/>
611 <expand macro="mod_option" value="DimethLys8"/>
612 <expand macro="mod_option" value="DimethNter8"/>
613 <expand macro="mod_option" value="18O"/>
614 <expand macro="mod_option" value="ICAT-0"/>
615 <expand macro="mod_option" value="ICAT-9"/>
616 <expand macro="mod_option" value="ICPL-Lys0"/>
617 <expand macro="mod_option" value="ICPL-Nter0"/>
618 <expand macro="mod_option" value="ICPL-Lys4"/>
619 <expand macro="mod_option" value="ICPL-Nter4"/>
620 <expand macro="mod_option" value="ICPL-Lys6"/>
621 <expand macro="mod_option" value="ICPL-Nter6"/>
622 <expand macro="mod_option" value="ICPL-Lys10"/>
623 <expand macro="mod_option" value="ICPL-Nter10"/>
624 <expand macro="mod_option" value="mTRAQ-Lys0"/>
625 <expand macro="mod_option" value="mTRAQ-Nter0"/>
626 <expand macro="mod_option" value="mTRAQ-Lys4"/>
627 <expand macro="mod_option" value="mTRAQ-Nter4"/>
628 <expand macro="mod_option" value="mTRAQ-Lys8"/>
629 <expand macro="mod_option" value="mTRAQ-Nter8"/>
630 <expand macro="mod_option" value="DimethLys2"/>
631 <expand macro="mod_option" value="DimethNter2"/>
632 <expand macro="mod_option" value="DimethLys6"/>
633 <expand macro="mod_option" value="DimethNter6"/>
634 <expand macro="mod_option" value="Leu7"/>
635 <expand macro="mod_option" value="Ile7"/>
636 </xml>
637
638 <xml name="proteases">
639 <expand macro="mod_option" value="Trypsin"/>
640 <expand macro="mod_option" value="Trypsin/P"/>
641 <expand macro="mod_option" value="LysC"/>
642 <expand macro="mod_option" value="LysC/P"/>
643 <expand macro="mod_option" value="D.P"/>
644 <expand macro="mod_option" value="ArgC"/>
645 <expand macro="mod_option" value="AspC"/>
646 <expand macro="mod_option" value="GluC"/>
647 <expand macro="mod_option" value="GluN"/>
648 <expand macro="mod_option" value="AspN"/>
649 <expand macro="mod_option" value="LysN"/>
650 <expand macro="mod_option" value="Chymotrypsin+"/>
651 <expand macro="mod_option" value="Chymotrypsin"/>
652 </xml>
653
654 <xml name="iso_labels">
655 <expand macro="mod_option" value="iTRAQ4plex-Nter114"/>
656 <expand macro="mod_option" value="iTRAQ4plex-Nter115"/>
657 <expand macro="mod_option" value="iTRAQ4plex-Nter116"/>
658 <expand macro="mod_option" value="iTRAQ4plex-Nter117"/>
659 <expand macro="mod_option" value="iTRAQ4plex-Lys114"/>
660 <expand macro="mod_option" value="iTRAQ4plex-Lys115"/>
661 <expand macro="mod_option" value="iTRAQ4plex-Lys116"/>
662 <expand macro="mod_option" value="iTRAQ4plex-Lys117"/>
663 <expand macro="mod_option" value="iTRAQ8plex-Nter113"/>
664 <expand macro="mod_option" value="iTRAQ8plex-Nter114"/>
665 <expand macro="mod_option" value="iTRAQ8plex-Nter115"/>
666 <expand macro="mod_option" value="iTRAQ8plex-Nter116"/>
667 <expand macro="mod_option" value="iTRAQ8plex-Nter117"/>
668 <expand macro="mod_option" value="iTRAQ8plex-Nter118"/>
669 <expand macro="mod_option" value="iTRAQ8plex-Nter119"/>
670 <expand macro="mod_option" value="iTRAQ8plex-Nter121"/>
671 <expand macro="mod_option" value="iTRAQ8plex-Lys113"/>
672 <expand macro="mod_option" value="iTRAQ8plex-Lys114"/>
673 <expand macro="mod_option" value="iTRAQ8plex-Lys115"/>
674 <expand macro="mod_option" value="iTRAQ8plex-Lys116"/>
675 <expand macro="mod_option" value="iTRAQ8plex-Lys117"/>
676 <expand macro="mod_option" value="iTRAQ8plex-Lys118"/>
677 <expand macro="mod_option" value="iTRAQ8plex-Lys119"/>
678 <expand macro="mod_option" value="iTRAQ8plex-Lys121"/>
679 <expand macro="mod_option" value="TMT2plex-Nter126"/>
680 <expand macro="mod_option" value="TMT2plex-Nter127"/>
681 <expand macro="mod_option" value="TMT2plex-Lys126"/>
682 <expand macro="mod_option" value="TMT2plex-Lys127"/>
683 <expand macro="mod_option" value="TMT6plex-Nter126"/>
684 <expand macro="mod_option" value="TMT6plex-Nter127"/>
685 <expand macro="mod_option" value="TMT6plex-Nter128"/>
686 <expand macro="mod_option" value="TMT6plex-Nter129"/>
687 <expand macro="mod_option" value="TMT6plex-Nter130"/>
688 <expand macro="mod_option" value="TMT6plex-Nter131"/>
689 <expand macro="mod_option" value="TMT8plex-Nter126C"/>
690 <expand macro="mod_option" value="TMT8plex-Nter127N"/>
691 <expand macro="mod_option" value="TMT8plex-Nter127C"/>
692 <expand macro="mod_option" value="TMT8plex-Nter128C"/>
693 <expand macro="mod_option" value="TMT8plex-Nter129N"/>
694 <expand macro="mod_option" value="TMT8plex-Nter129C"/>
695 <expand macro="mod_option" value="TMT8plex-Nter130C"/>
696 <expand macro="mod_option" value="TMT8plex-Nter131N"/>
697 <expand macro="mod_option" value="TMT10plex-Nter126C"/>
698 <expand macro="mod_option" value="TMT10plex-Nter127N"/>
699 <expand macro="mod_option" value="TMT10plex-Nter127C"/>
700 <expand macro="mod_option" value="TMT10plex-Nter128N"/>
701 <expand macro="mod_option" value="TMT10plex-Nter128C"/>
702 <expand macro="mod_option" value="TMT10plex-Nter129N"/>
703 <expand macro="mod_option" value="TMT10plex-Nter129C"/>
704 <expand macro="mod_option" value="TMT10plex-Nter130N"/>
705 <expand macro="mod_option" value="TMT10plex-Nter130C"/>
706 <expand macro="mod_option" value="TMT10plex-Nter131N"/>
707 <expand macro="mod_option" value="TMT11plex-Nter131C"/>
708 <expand macro="mod_option" value="TMT6plex-Lys126"/>
709 <expand macro="mod_option" value="TMT6plex-Lys127"/>
710 <expand macro="mod_option" value="TMT6plex-Lys128"/>
711 <expand macro="mod_option" value="TMT6plex-Lys129"/>
712 <expand macro="mod_option" value="TMT6plex-Lys130"/>
713 <expand macro="mod_option" value="TMT6plex-Lys131"/>
714 <expand macro="mod_option" value="TMT8plex-Lys126C"/>
715 <expand macro="mod_option" value="TMT8plex-Lys127N"/>
716 <expand macro="mod_option" value="TMT8plex-Lys127C"/>
717 <expand macro="mod_option" value="TMT8plex-Lys128C"/>
718 <expand macro="mod_option" value="TMT8plex-Lys129N"/>
719 <expand macro="mod_option" value="TMT8plex-Lys129C"/>
720 <expand macro="mod_option" value="TMT8plex-Lys130C"/>
721 <expand macro="mod_option" value="TMT8plex-Lys131N"/>
722 <expand macro="mod_option" value="TMT10plex-Lys126C"/>
723 <expand macro="mod_option" value="TMT10plex-Lys127N"/>
724 <expand macro="mod_option" value="TMT10plex-Lys127C"/>
725 <expand macro="mod_option" value="TMT10plex-Lys128N"/>
726 <expand macro="mod_option" value="TMT10plex-Lys128C"/>
727 <expand macro="mod_option" value="TMT10plex-Lys129N"/>
728 <expand macro="mod_option" value="TMT10plex-Lys129C"/>
729 <expand macro="mod_option" value="TMT10plex-Lys130N"/>
730 <expand macro="mod_option" value="TMT10plex-Lys130C"/>
731 <expand macro="mod_option" value="TMT10plex-Lys131N"/>
732 <expand macro="mod_option" value="TMT11plex-Lys131C"/>
733 <expand macro="mod_option" value="iodoTMT6plex-Cys126"/>
734 <expand macro="mod_option" value="iodoTMT6plex-Cys127"/>
735 <expand macro="mod_option" value="iodoTMT6plex-Cys128"/>
736 <expand macro="mod_option" value="iodoTMT6plex-Cys129"/>
737 <expand macro="mod_option" value="iodoTMT6plex-Cys130"/>
738 <expand macro="mod_option" value="iodoTMT6plex-Cys131"/>
739 </xml>
740
741 <xml name="citations">
742 <citations>
743 <citation type="bibtex">
744 @article{cox2008maxquant,
745 title={MaxQuant enables high peptide identification rates, individualized
746 ppb-range mass accuracies and proteome-wide protein quantification},
747 author={Cox, J{\"u}rgen and Mann, Matthias},
748 journal={Nature biotechnology},
749 volume={26},
750 number={12},
751 pages={1367},
752 year={2008},
753 publisher={Nature Publishing Group}
754 }
755 </citation>
756 <citation type="bibtex">
757 @article{tyanova2016maxquant,
758 title={The MaxQuant computational platform for mass
759 spectrometry-based shotgun proteomics},
760 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
761 journal={Nature protocols},
762 volume={11},
763 number={12},
764 pages={2301},
765 year={2016},
766 publisher={Nature Publishing Group}
767 }
768 </citation>
769 <citation type="doi">10.1021/acs.jproteome.5b00780</citation>
770 </citations>
12 </xml> 771 </xml>
13 </macros> 772 </macros>
14