| Next changeset 1:8bac3cc5c5de (2019-07-20) |
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LICENSE README.md README_GALAXYP.md README_REPO.md augment_maxquant_mods.py build_mods_loc.py build_proteases_loc.py extended_modifications.xml maxquant.xml maxquant_mods.loc maxquant_mods.loc.sample maxquant_mods.loc.sample.default maxquant_mods.loc.sample.extended maxquant_proteases.loc maxquant_proteases.loc.sample maxquant_wrapper.py modifications.xml proteases.xml unimod.xml update.sh |
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| diff -r 000000000000 -r d4b6c9eae635 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Fri May 10 17:22:51 2013 -0400 |
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| @@ -0,0 +1,11 @@ +--2012-09-19 08:46:18-- http://www.apache.org/licenses/LICENSE-2.0.txt +Resolving www.apache.org... 140.211.11.131, 192.87.106.229, 2001:610:1:80bc:192:87:106:229 +Connecting to www.apache.org|140.211.11.131|:80... connected. +HTTP request sent, awaiting response... 200 OK +Length: 11358 (11K) [text/plain] +Saving to: “LICENSE-2.0.txt” + + 0K .......... . 100% 200K=0.06s + +2012-09-19 08:46:18 (200 KB/s) - “LICENSE-2.0.txt” saved [11358/11358] + |
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| diff -r 000000000000 -r d4b6c9eae635 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 10 17:22:51 2013 -0400 |
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| @@ -0,0 +1,34 @@ +Tool wrapper for MaxQuant. + +MaxQuant is a Windows only program and so you will likely need to +deploy this tool to run on a remote Windows system via the LWR +(https://lwr.readthedocs.org). + +The sample mods file maxquant_mods.loc.sample corresponds to the +default modifications MaxQuant is configured with. The Galaxy-P +project uses a MaxQuant that has been extended with all of Unimod. To +modify MaxQuant in this fashion replace MaxQuant's modifications.xml +file with the extended_modifications.xml distributed with this tool +and configure Galaxy with the maxquant_mods.loc.sample.extended loc +file.# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. |
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| diff -r 000000000000 -r d4b6c9eae635 README_GALAXYP.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Fri May 10 17:22:51 2013 -0400 |
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| @@ -0,0 +1,22 @@ +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta. |
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| diff -r 000000000000 -r d4b6c9eae635 README_REPO.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Fri May 10 17:22:51 2013 -0400 |
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| @@ -0,0 +1,13 @@ +Tool wrapper for MaxQuant. + +MaxQuant is a Windows only program and so you will likely need to +deploy this tool to run on a remote Windows system via the LWR +(https://lwr.readthedocs.org). + +The sample mods file maxquant_mods.loc.sample corresponds to the +default modifications MaxQuant is configured with. The Galaxy-P +project uses a MaxQuant that has been extended with all of Unimod. To +modify MaxQuant in this fashion replace MaxQuant's modifications.xml +file with the extended_modifications.xml distributed with this tool +and configure Galaxy with the maxquant_mods.loc.sample.extended loc +file. \ No newline at end of file |
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| diff -r 000000000000 -r d4b6c9eae635 augment_maxquant_mods.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augment_maxquant_mods.py Fri May 10 17:22:51 2013 -0400 |
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| @@ -0,0 +1,166 @@ +#!/usr/bin/env python +""" +Usage: + python augment_maxquant_mods.py + +Assuming Unimod XML file (unimod.xml) and stock MaxQuant modifications +file (modifications.xml) are in this same directory, this script will +create a new MaxQuant modifications file (extended_modifications.xml) +with an a new modification for each unimod entry. These new entires +will be suffixed with [Unimod] to distinguish them from existing +MaxQuant entries. This file should be copied to +<MaxQuant Path>\bin\conf\modifications.xml + +""" +import xml.etree.ElementTree as ET +import re + +FAKE_DATE = "2012-06-11T21:21:24.4946343+02:00" + +POSITION_MAP = { + "Anywhere": "anywhere", + "Any N-term": "anyNterm", + "Any C-term": "anyCterm", + "Protein N-term": "proteinNterm", + "Protein C-term": "proteinCterm", +} + +unimod_tree = ET.parse('unimod.xml') +unimod_ns = '{http://www.unimod.org/xmlns/schema/unimod_2}' +unimod_modifications_el = unimod_tree.getroot().find('%smodifications' % unimod_ns) +mq_tree = ET.parse("modifications.xml") +mq_root = mq_tree.getroot() + + +def to_label(title, site): + return "%s (%s) [Unimod]" % (title, site) + + +def copy_modification(unimod_modification): + if unimod_modification.hidden: + return False + if unimod_modification.delta_el is None: + return False + comp_array = unimod_modification.composition_array + for aa, count in comp_array: + if len(aa) > 1 and aa not in COMP_REPLACES.keys(): + # Complex stuff like Hep, that I cannot translate into MaxQuant. + return False + return True + + +COMP_REPLACES = { + "15N": "Nx", + "13C": "Cx", + "18O": "Ox", + "2H": "Hx", +} + +## HEP? + + +def convert_composition(unimod_composition): + """ + Convert Unimod representation of composition to MaxQuant + """ + composition = unimod_composition + for key, value in COMP_REPLACES.iteritems(): + composition = composition.replace(key, value) + print composition + return composition + + +def populate_modification(modification, unimod_modification): + """ + Copy unimod entry ``unimod_modification`` to MaxQuant entry ``modification``. + """ + attrib = modification.attrib + attrib["create_date"] = FAKE_DATE + attrib["last_modified_date"] = FAKE_DATE + attrib["reporterCorrectionM1"] = str(0) + attrib["reporterCorrectionM2"] = str(0) + attrib["reporterCorrectionP1"] = str(0) + attrib["reporterCorrectionP2"] = str(0) + attrib["user"] = "build_mods_script" + label = unimod_modification.label + attrib["title"] = label + attrib["description"] = label + attrib["composition"] = convert_composition(unimod_modification.raw_composition) + unimod_position = unimod_modification.position + maxquant_position = POSITION_MAP[unimod_position] + assert maxquant_position != None + position_el = ET.SubElement(modification, "position") + position_el.text = maxquant_position + modification_site_el = ET.SubElement(modification, "modification_site") + modification_site_el.attrib["index"] = "0" + unimod_site = unimod_modification.site + modification_site_el.attrib["site"] = "-" if len(unimod_site) > 1 else unimod_site + type_el = ET.SubElement(modification, "type") + type_el.text = "standard" + return modification + + +class UnimodModification: + + def __init__(self, modification, specificity): + self.modification = modification + self.specificity = specificity + + @property + def title(self): + return self.modification.attrib["title"] + + @property + def site(self): + return self.specificity.attrib["site"] + + @property + def label(self): + return "%s (%s) [Unimod]" % (self.title, self.site) + + @property + def delta_el(self): + return self.modification.find("%sdelta" % unimod_ns) + + @property + def raw_composition(self): + return self.delta_el.attrib["composition"] + + @property + def composition_array(self): + raw_composition = self.raw_composition + aa_and_counts = re.split("\s+", raw_composition) + comp_array = [] + for aa_and_count in aa_and_counts: + match = re.match(r"(\w+)(\((-?\d+)\))?", aa_and_count) + aa = match.group(1) + count = match.group(3) or 1 + comp_array.append((aa, count)) + return comp_array + + @property + def position(self): + return self.specificity.attrib["position"] + + @property + def hidden(self): + return self.specificity.attrib["hidden"] == "true" + +unimod_modifications = [] +for mod in unimod_modifications_el.findall('%smod' % unimod_ns): + for specificity in mod.findall('%sspecificity' % unimod_ns): + unimod_modifications.append(UnimodModification(mod, specificity)) + +max_index = 0 +for modification in mq_root.getchildren(): + index = int(modification.attrib["index"]) + max_index = max(max_index, index) + +for unimod_modification in unimod_modifications: + if copy_modification(unimod_modification): + print unimod_modification.composition_array + max_index += 1 + modification = ET.SubElement(mq_root, "modification", attrib={"index": str(max_index)}) + populate_modification(modification, unimod_modification) + +mq_tree.write("extended_modifications.xml") |
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| diff -r 000000000000 -r d4b6c9eae635 build_mods_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_mods_loc.py Fri May 10 17:22:51 2013 -0400 |
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| @@ -0,0 +1,17 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +mods_path = "extended_modifications.xml" + +if not exists(mods_path): + mods_path = "modifications.xml" + +tree = ET.parse(mods_path) +modifications_el = tree.getroot() + +with open("maxquant_mods.loc", "w") as output: + for mod in modifications_el.getchildren(): + if mod.find("type").text.strip() == "standard": + output.write("%s\n" % mod.attrib["title"]) |
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| diff -r 000000000000 -r d4b6c9eae635 build_proteases_loc.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build_proteases_loc.py Fri May 10 17:22:51 2013 -0400 |
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| @@ -0,0 +1,14 @@ +#!/usr/bin/env python + +import xml.etree.ElementTree as ET +from os.path import exists + +proteases_path = "proteases.xml" + +tree = ET.parse(proteases_path) +proteases_el = tree.getroot() + +with open("maxquant_proteases.loc", "w") as output: + for protease in proteases_el.getchildren(): + output.write("%s\n" % protease.attrib["name"]) + |
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| diff -r 000000000000 -r d4b6c9eae635 extended_modifications.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extended_modifications.xml Fri May 10 17:22:51 2013 -0400 |
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| b'@@ -0,0 +1,2579 @@\n+<modifications>\n+ <modification composition="C(2) H(2) O" create_date="2010-01-19T13:25:24.82357+01:00" description="Acetylation" index="0" last_modified_date="2010-01-19T14:15:40.2445414+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Acetyl (K)" user="neuhause">\n+ <position>notCterm</position>\n+ <modification_site index="0" site="K">\n+ <diagnostic_collection>\n+ <diagnostic composition="C(7) H(11) O N" name="acK*" shortname="acK*" />\n+ <diagnostic composition="C(7) H(14) O N(2)" name="acK" shortname="acK" />\n+ </diagnostic_collection>\n+ </modification_site>\n+ <type>standard</type>\n+ </modification>\n+ <modification composition="C(2) H(2) O" create_date="2010-01-19T14:27:34.5843488+01:00" description="Acetylation" index="1" last_modified_date="2010-01-19T14:28:09.7383488+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Acetyl (Protein N-term)" user="neuhause">\n+ <position>proteinNterm</position>\n+ <modification_site index="0" site="-" />\n+ <type>standard</type>\n+ </modification>\n+ <modification composition="C(2) H(3) N O" create_date="2010-01-19T15:54:02.1976309+01:00" description="Iodoacetamide derivative" index="2" last_modified_date="2010-01-19T15:55:13.1353165+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Carbamidomethyl (C)" user="neuhause">\n+ <position>anywhere</position>\n+ <modification_site index="0" site="C" />\n+ <type>standard</type>\n+ </modification>\n+ <modification composition="O " create_date="2010-01-19T14:29:05.2191728+01:00" description="Oxidation" index="3" last_modified_date="2010-01-19T20:38:21.9609829+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Oxidation (M)" user="neuhause">\n+ <position>anywhere</position>\n+ <modification_site index="0" site="M" />\n+ <type>standard</type>\n+ </modification>\n+ <modification composition="H O(3) P" create_date="2010-01-19T14:34:50.0721008+01:00" description="Phosphorylation" index="4" last_modified_date="2010-01-19T20:39:28.1471599+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Phospho (STY)" user="neuhause">\n+ <position>anywhere</position>\n+ <modification_site index="0" site="S">\n+ <neutralloss_collection>\n+ <neutralloss composition="H(3) O(4) P" name="H(3) O(4) P" shortname="H3 O4 P" />\n+ </neutralloss_collection>\n+ </modification_site>\n+ <modification_site index="1" site="T">\n+ <neutralloss_collection>\n+ <neutralloss composition="H(3) O(4) P" name="H(3) O(4) P" shortname="H3 O4 P" />\n+ </neutralloss_collection>\n+ </modification_site>\n+ <modification_site index="2" site="Y">\n+ <diagnostic_collection>\n+ <diagnostic composition="C(8) H(10) O(4) N P" name="C(8) H(10) O(4) N P" shortname="pY" />\n+ </diagnostic_collection>\n+ </modification_site>\n+ <type>standard</type>\n+ </modification>\n+ <modification composition="Cx(6) C(-6)" create_date="2010-01-19T14:37:21.2757206+01:00" description="Arginine-13C6 (R-13C6)" index="5" last_modified_date="2010-01-23T19:17:45.328125+01:00" multi_modification="false" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Arg6" user="cox">\n+ <position>anywhere</position>\n+ <modification_site index="0" site="R" />\n+ <type>label</type>\n+ </modification>\n+ <modification composition="Cx(6) Nx(4) C(-6) N(-4)" create_date="2010-01-19T14:38:45.7906712+01:00" des'..b'rrectionP2="0" title="MG-H1 (R) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="R" /><type>standard</type></modification><modification composition="C(2) O" create_date="2012-06-11T21:21:24.4946343+02:00" description="G-H1 (R) [Unimod]" index="1300" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="G-H1 (R) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="R" /><type>standard</type></modification><modification composition="H(6) C(-2) Cx(6) Nx(2) O(2)" create_date="2012-06-11T21:21:24.4946343+02:00" description="Label:13C(6)15N(2)+GlyGly (K) [Unimod]" index="1301" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Label:13C(6)15N(2)+GlyGly (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(-1) Hx(4) Cx(6) N O" create_date="2012-06-11T21:21:24.4946343+02:00" description="ICPL:13C(6)2H(4) (N-term) [Unimod]" index="1302" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="ICPL:13C(6)2H(4) (N-term) [Unimod]" user="build_mods_script"><position>anyNterm</position><modification_site index="0" site="-" /><type>standard</type></modification><modification composition="H(-1) Hx(4) Cx(6) N O" create_date="2012-06-11T21:21:24.4946343+02:00" description="ICPL:13C(6)2H(4) (K) [Unimod]" index="1303" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="ICPL:13C(6)2H(4) (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(-1) Hx(4) Cx(6) N O" create_date="2012-06-11T21:21:24.4946343+02:00" description="ICPL:13C(6)2H(4) (N-term) [Unimod]" index="1304" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="ICPL:13C(6)2H(4) (N-term) [Unimod]" user="build_mods_script"><position>proteinNterm</position><modification_site index="0" site="-" /><type>standard</type></modification><modification composition="H(39) C(23) N(9) O(11)" create_date="2012-06-11T21:21:24.4946343+02:00" description="QQQTGG (K) [Unimod]" index="1305" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="QQQTGG (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(38) C(23) N(8) O(12)" create_date="2012-06-11T21:21:24.4946343+02:00" description="QEQTGG (K) [Unimod]" index="1306" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="QEQTGG (K) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="K" /><type>standard</type></modification><modification composition="H(21) B C(20) N(4) O(3) F(2)" create_date="2012-06-11T21:21:24.4946343+02:00" description="Bodipy (C) [Unimod]" index="1307" last_modified_date="2012-06-11T21:21:24.4946343+02:00" reporterCorrectionM1="0" reporterCorrectionM2="0" reporterCorrectionP1="0" reporterCorrectionP2="0" title="Bodipy (C) [Unimod]" user="build_mods_script"><position>anywhere</position><modification_site index="0" site="C" /><type>standard</type></modification></modifications>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r d4b6c9eae635 maxquant.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant.xml Fri May 10 17:22:51 2013 -0400 |
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| b'@@ -0,0 +1,331 @@\n+<tool id="maxquant" version="0.1.0" name="MaxQuant">\n+ <description>\n+ </description>\n+ <requirements>\n+ <requirement>maxquant</requirement>\n+ <requirement type="platform">windows</requirement>\n+ </requirements>\n+ <configfiles>\n+ <configfile name="inputs_config">##Describe inputs\n+#set $type = str($analysis_type.type)\n+#if $type == "single"\n+#set $groups = [$analysis_type]\n+#elif $type == "multi_same"\n+#set $groups = $analysis_type.groups\n+#end if\n+#for $i, $group in enumerate($groups)\n+num:${str(i + 1)}\n+#for $input in $group.inputs\n+name:${input.display_name}\n+path:${input}\n+#end for\n+#end for\n+</configfile>\n+ </configfiles>\n+ <command interpreter="python">maxquant_wrapper.py \n+ --input_groups=$inputs_config\n+ --database="${database}"\n+ --database_name="${database.name}"\n+ --protease=$analysis_type.protease\n+ --first_search_tol=$analysis_type.first_search_tol\n+ --main_search_tol=$analysis_type.main_search_tol\n+ --max_missed_cleavages=$analysis_type.max_missed_cleavages\n+ --max_n_mods=$analysis_type.max_n_mods\n+ --variable_mods="${analysis_type.variable_modifications or \'\'}"\n+ #if $analysis_type.advanced_group_parameters.specify\n+ --do_mass_filtering=$analysis_type.advanced_group_parameters.do_mass_filtering\n+ --max_charge=$analysis_type.advanced_group_parameters.max_charge\n+ #end if\n+ #set $run = $analysis_type.run\n+ #set $lcms_run_type = $run.lcms_run_type\n+ --lcms_run_type=$lcms_run_type\n+ #if str($lcms_run_type) != "3"\n+ ## i.e. is not reporter ion type\n+ #if $run.labels_conditional.labeled\n+ #for $label_group in $run.labels_conditional.label_groups\n+ --labels="${label_group.labels or \'\'}"\n+ #end for\n+ --max_labeled_aa=$run.labels_conditional.max_labeled_aa\n+ #end if\n+ #else\n+ --reporter_type=$run.reporter_type\n+ #end if \n+ #set $sp = $advanced_sequence_parameters\n+ #if $sp.specify\n+ --include_contamiants=${str(sp[\'include_contamiants\']).lower()}\n+ --equal_il=${str(sp[\'equal_il\']).lower()}\n+ --randomize=${str(sp[\'randomize\'])}\n+ #end if\n+ #if $quantification.specify\n+ #set $restrict = $quantification.restrict.restrict_protein_quantification\n+ --restrict_protein_quantification=${str(restrict).lower()}\n+ #if $quantification.restrict.restrict_protein_quantification\n+ --restrict_mods="${quantification.restrict.restrict_modifications or \'\'}"\n+ #end if\n+ --quant_mode=$quantification.quant_mode\n+ --use_counterparts=$quantification.use_counterparts\n+ --min_ratio_count=$quantification.min_ratio_count\n+ #end if\n+ #if $site_quantification.specify\n+ --site_quant_mode=$site_quantification.site_quant_mode\n+ --use_norm_ratios_for_occupancy=$site_quantification.use_norm_ratios_for_occupancy\n+ #end if\n+ #set $identification_type = str($identification.options_type)\n+ #if $identification_type != "none"\n+ --protein_fdr=$identification.protein_fdr\n+ --peptide_fdr=$identification.peptide_fdr\n+ --site_fdr=$identification.site_fdr\n+ #if $identification_type != "simple"\n+ --peptide_pep=$identification.peptide_pep\n+ #end if\n+ #end if\n+ #if $misc.specify\n+ --re_quantify="$misc.re_quantify"\n+ #end if\n+ --fixed_mods="${fixed_modifications or \'\'}"\n+ --output_protein_groups=$output_protein_groups\n+ --output_peptides=$output_peptides\n+ --output_evidence=$output_evidence\n+ --output_parameters=$output_parameters\n+ --output_msms=$output_msms\n+ --output_mqpar=$output_mqpar\n+ </command>\n+ <macros>\n+ <macro name="input_param">\n+ <param format="raw" multiple="true" name="inputs" type="data" label="RAW Inputs" help="" />\n+ </macro>\n+ <macro name="mod_opts">\n+ <options from_file="maxquant_mods.loc">\n+ <column name="name" index="0"/>\n+ <column name="value" index="0" />\n+ </options>\n+ <sanitizer>\n+ <valid>\n+ <add value="<"/>\n+ <add value=">"/>\n+ <add '..b' </when>\n+ </conditional>\n+ <param name="quant_mode" type="select" label="Protein Quantification Mode">\n+ <option value="0">Use all peptides</option>\n+ <option value="1" selected="true">Use razor and unique peptides</option>\n+ <option value="2">Use unique peptides</option>\n+ </param>\n+ <param name="use_counterparts" type="boolean" label="Discard Unmodified Counterpart Peptides." checked="true" truevalue="false" falsevalue="true" />\n+ <param name="min_ratio_count" label="Minimum Ratio Count" value="2" type="integer" />\n+ </when>\n+ </conditional>\n+ </macro>\n+ <macro name="simple_identification_params">\n+ <param name="protein_fdr" label="Protein FDR" value="0.01" type="float" />\n+ <param name="peptide_fdr" label="Peptide FDR" value="0.01" type="float" />\n+ <param name="site_fdr" label="Protein FDR" value="0.01" type="float" />\n+ </macro>\n+ <macro name="advanced_identification_params">\n+ <param name="peptide_pep" label="Max Peptide PEP" value="1" type="float" />\n+ <!-- TODO: Apply site FDR seperately (boolean), Min peptides, Min Score, \n+ min peptide length, min razor + unique peptides, filter labeled aa,\n+ min unique peptides, second peptides (boolean true) -->\n+ </macro>\n+ <macro name="misc_conditional">\n+ <conditional name="misc">\n+ <param name="specify" type="boolean" label="Specify Misc Parameters" checked="false" />\n+ <when value="false">\n+ </when>\n+ <when value="true">\n+ <param name="re_quantify" type="boolean" label="Re-quantify" checked="true" truevalue="true" falsevalue="false" />\n+ <!--\n+ "Keep low-scoring versions of identified peptides" 0 = No, 1 only within parameters groups, 2 = Also between parameter groups.\n+ Match Between Runs: bool\n+ Time window (minutes): 2\n+ Label-free quantification:\n+ LFO min ratio count 2\n+ Fast LFQ\n+ iBAQ\n+ Log fit\n+ -->\n+ </when>\n+ </conditional>\n+ </macro>\n+ </macros>\n+ <inputs>\n+ <conditional name="analysis_type">\n+ <param name="type" type="select" value="single" help="The wrapper has not yet implemented multiple groups with different parameters">\n+ <option value="single">Single Group</option>\n+ <option value="multi_same">Multi-Group Identical Parameters</option>\n+ </param>\n+ <when value="multi_same">\n+ <repeat name="groups">\n+ <expand macro="input_param" />\n+ </repeat>\n+\t <expand macro="group_params" />\n+ </when>\n+ <when value="single">\n+ <expand macro="input_param" />\n+ <expand macro="group_params" />\n+ </when>\n+ </conditional>\n+ <param format="fasta" name="database" type="data" label="FASTA Database" help="" />\n+ <expand macro="advanced_sequences_conditional" />\n+ <param name="fixed_modifications" label="Fixed Modifications" type="select" multiple="true">\n+ <expand macro="mod_opts" />\n+ </param>\n+ <expand macro="identification_conditional" />\n+ <expand macro="protein_quantification_conditional" />\n+ <expand macro="site_quantification_conditional" />\n+ <expand macro="misc_conditional" />\n+ </inputs>\n+ <outputs>\n+ <data format="tabular" name="output_protein_groups" label="MaxQuant Protein Groups for ${on_string}"/>\n+ <data format="tabular" name="output_peptides" label="MaxQuant Peptides for ${on_string}"/>\n+ <data format="tabular" name="output_evidence" label="MaxQuant Evidence for ${on_string}"/>\n+ <data format="tabular" name="output_parameters" label="MaxQuant Tabular Parameters for ${on_string}"/>\n+ <data format="tabular" name="output_msms" label="MaxQuant MSMS for ${on_string}"/>\n+ <data format="tabular" name="output_mqpar" label="MaxQuant Parameters XML for ${on_string}"/>\n+ </outputs>\n+ <help>\n+ </help>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc Fri May 10 17:22:51 2013 -0400 |
| [ |
| b'@@ -0,0 +1,1234 @@\n+Acetyl (K)\n+Acetyl (Protein N-term)\n+Carbamidomethyl (C)\n+Oxidation (M)\n+Phospho (STY)\n+GlyGly (K)\n+Methyl (KR)\n+Dimethyl (KR)\n+Trimethyl (K)\n+Pro5\n+Pro6\n+Glu->pyro-Glu\n+Gln->pyro-Glu\n+OHexNAc\n+QQTGG (K)\n+Deamidation (N)\n+Deamidation 18O (N)\n+Deamidation (NQ)\n+Ala->Arg\n+Ala->Asn\n+Ala->Asp\n+Ala->Cys\n+Ala->Gln\n+Ala->Glu\n+Ala->Gly\n+Ala->His\n+Ala->Xle\n+Ala->Lys\n+Ala->Met\n+Ala->Phe\n+Ala->Pro\n+Ala->Ser\n+Ala->Thr\n+Ala->Trp\n+Ala->Tyr\n+Ala->Val\n+Arg->Ala\n+Arg->Asn\n+Arg->Asp\n+Arg->Cys\n+Arg->Gln\n+Arg->Glu\n+Arg->Gly\n+Arg->His\n+Arg->Lys\n+Arg->Met\n+Arg->Phe\n+Arg->Pro\n+Arg->Ser\n+Arg->Thr\n+Arg->Trp\n+Arg->Tyr\n+Arg->Val\n+Arg->Xle\n+Asn->Ala\n+Asn->Arg\n+Asn->Asp\n+Asn->Cys\n+Asn->Gln\n+Asn->Glu\n+Asn->Gly\n+Asn->His\n+Asn->Lys\n+Asn->Met\n+Asn->Phe\n+Asn->Pro\n+Asn->Ser\n+Asn->Thr\n+Asn->Trp\n+Asn->Tyr\n+Asn->Val\n+Asn->Xle\n+Asp->Ala\n+Asp->Arg\n+Asp->Asn\n+Asp->Cys\n+Asp->Gln\n+Asp->Glu\n+Asp->Gly\n+Asp->His\n+Asp->Lys\n+Asp->Met\n+Asp->Phe\n+Asp->Pro\n+Asp->Ser\n+Asp->Thr\n+Asp->Trp\n+Asp->Tyr\n+Asp->Val\n+Asp->Xle\n+Cys->Ala\n+Cys->Arg\n+Cys->Asn\n+Cys->Asp\n+Cys->Gln\n+Cys->Glu\n+Cys->Gly\n+Cys->His\n+Cys->Lys\n+Cys->Met\n+Cys->Phe\n+Cys->Pro\n+Cys->Ser\n+Cys->Thr\n+Cys->Trp\n+Cys->Tyr\n+Cys->Val\n+Cys->Xle\n+Gln->Ala\n+Gln->Arg\n+Gln->Asn\n+Gln->Asp\n+Gln->Cys\n+Gln->Glu\n+Gln->Gly\n+Gln->His\n+Gln->Lys\n+Gln->Met\n+Gln->Phe\n+Gln->Pro\n+Gln->Ser\n+Gln->Thr\n+Gln->Trp\n+Gln->Tyr\n+Gln->Val\n+Gln->Xle\n+Glu->Ala\n+Glu->Arg\n+Glu->Asn\n+Glu->Asp\n+Glu->Cys\n+Glu->Gln\n+Glu->Gly\n+Glu->His\n+Glu->Lys\n+Glu->Met\n+Glu->Phe\n+Glu->Pro\n+Glu->Ser\n+Glu->Thr\n+Glu->Trp\n+Glu->Tyr\n+Glu->Val\n+Glu->Xle\n+Gly->Ala\n+Gly->Arg\n+Gly->Asn\n+Gly->Asp\n+Gly->Cys\n+Gly->Gln\n+Gly->Glu\n+Gly->His\n+Gly->Lys\n+Gly->Met\n+Gly->Phe\n+Gly->Pro\n+Gly->Ser\n+Gly->Thr\n+Gly->Trp\n+Gly->Tyr\n+Gly->Val\n+Gly->Xle\n+His->Ala\n+His->Arg\n+His->Asn\n+His->Asp\n+His->Cys\n+His->Gln\n+His->Glu\n+His->Gly\n+His->Lys\n+His->Met\n+His->Phe\n+His->Pro\n+His->Ser\n+His->Thr\n+His->Trp\n+His->Tyr\n+His->Val\n+His->Xle\n+Lys->Ala\n+Lys->Arg\n+Lys->Asn\n+Lys->Asp\n+Lys->Cys\n+Lys->Gln\n+Lys->Glu\n+Lys->Gly\n+Lys->His\n+Lys->Met\n+Lys->Phe\n+Lys->Pro\n+Lys->Ser\n+Lys->Thr\n+Lys->Trp\n+Lys->Tyr\n+Lys->Val\n+Lys->Xle\n+Met->Ala\n+Met->Arg\n+Met->Asn\n+Met->Asp\n+Met->Cys\n+Met->Gln\n+Met->Glu\n+Met->Gly\n+Met->His\n+Met->Lys\n+Met->Phe\n+Met->Pro\n+Met->Ser\n+Met->Thr\n+Met->Trp\n+Met->Tyr\n+Met->Val\n+Met->Xle\n+Phe->Ala\n+Phe->Arg\n+Phe->Asn\n+Phe->Asp\n+Phe->Cys\n+Phe->Gln\n+Phe->Glu\n+Phe->Gly\n+Phe->His\n+Phe->Lys\n+Phe->Met\n+Phe->Pro\n+Phe->Ser\n+Phe->Thr\n+Phe->Trp\n+Phe->Tyr\n+Phe->Val\n+Phe->Xle\n+Pro->Ala\n+Pro->Arg\n+Pro->Asn\n+Pro->Asp\n+Pro->Cys\n+Pro->Gln\n+Pro->Glu\n+Pro->Gly\n+Pro->His\n+Pro->Lys\n+Pro->Met\n+Pro->Phe\n+Pro->Ser\n+Pro->Thr\n+Pro->Trp\n+Pro->Tyr\n+Pro->Val\n+Pro->Xle\n+Ser->Ala\n+Ser->Arg\n+Ser->Asn\n+Ser->Asp\n+Ser->Cys\n+Ser->Gln\n+Ser->Glu\n+Ser->Gly\n+Ser->His\n+Ser->Lys\n+Ser->Met\n+Ser->Phe\n+Ser->Pro\n+Ser->Thr\n+Ser->Trp\n+Ser->Tyr\n+Ser->Val\n+Ser->Xle\n+Thr->Ala\n+Thr->Arg\n+Thr->Asn\n+Thr->Asp\n+Thr->Cys\n+Thr->Gln\n+Thr->Glu\n+Thr->Gly\n+Thr->His\n+Thr->Lys\n+Thr->Met\n+Thr->Phe\n+Thr->Pro\n+Thr->Ser\n+Thr->Trp\n+Thr->Tyr\n+Thr->Val\n+Thr->Xle\n+Trp->Ala\n+Trp->Arg\n+Trp->Asn\n+Trp->Asp\n+Trp->Cys\n+Trp->Gln\n+Trp->Glu\n+Trp->Gly\n+Trp->His\n+Trp->Lys\n+Trp->Met\n+Trp->Phe\n+Trp->Pro\n+Trp->Ser\n+Trp->Thr\n+Trp->Tyr\n+Trp->Val\n+Trp->Xle\n+Tyr->Ala\n+Tyr->Arg\n+Tyr->Asn\n+Tyr->Asp\n+Tyr->Cys\n+Tyr->Gln\n+Tyr->Glu\n+Tyr->Gly\n+Tyr->His\n+Tyr->Lys\n+Tyr->Met\n+Tyr->Phe\n+Tyr->Pro\n+Tyr->Ser\n+Tyr->Thr\n+Tyr->Trp\n+Tyr->Val\n+Tyr->Xle\n+Val->Ala\n+Val->Arg\n+Val->Asn\n+Val->Asp\n+Val->Cys\n+Val->Gln\n+Val->Glu\n+Val->Gly\n+Val->His\n+Val->Lys\n+Val->Met\n+Val->Phe\n+Val->Pro\n+Val->Ser\n+Val->Thr\n+Val->Trp\n+Val->Tyr\n+Val->Xle\n+Xle->Ala\n+Xle->Arg\n+Xle->Asn\n+Xle->Asp\n+Xle->Cys\n+Xle->Gln\n+Xle->Glu\n+Xle->Gly\n+Xle->His\n+Xle->Lys\n+Xle->Met\n+Xle->Phe\n+Xle->Pro\n+Xle->Ser\n+Xle->Thr\n+Xle->Trp\n+Xle->Tyr\n+Xle->Val\n+CamCys->Ala\n+CamCys->Arg\n+CamCys->Asn\n+CamCys->Asp\n+CamCys->Gln\n+CamCys->Glu\n+CamCys->Gly\n+CamCys->His\n+CamCys->Lys\n+CamCys->Met\n+CamCys->Phe\n+CamCys->Pro\n+CamCys->Ser\n+CamCys->Thr\n+CamCys->Trp\n+CamCys->Tyr\n+CamCys->Val\n+CamCys->Xle\n+Ala->CamCys\n+Arg->CamCys\n+Asn->CamCys\n+Asp->CamCys\n+Gln->CamCys\n'..b'r->Pro (T) [Unimod]\n+Thr->Met (T) [Unimod]\n+Thr->Ile (T) [Unimod]\n+Thr->Arg (T) [Unimod]\n+Val->Phe (V) [Unimod]\n+Val->Ala (V) [Unimod]\n+Val->Glu (V) [Unimod]\n+Val->Met (V) [Unimod]\n+Val->Asp (V) [Unimod]\n+Val->Ile (V) [Unimod]\n+Val->Gly (V) [Unimod]\n+Trp->Ser (W) [Unimod]\n+Trp->Cys (W) [Unimod]\n+Trp->Arg (W) [Unimod]\n+Trp->Gly (W) [Unimod]\n+Trp->Leu (W) [Unimod]\n+Tyr->Phe (Y) [Unimod]\n+Tyr->Ser (Y) [Unimod]\n+Tyr->Asn (Y) [Unimod]\n+Tyr->His (Y) [Unimod]\n+Tyr->Asp (Y) [Unimod]\n+Tyr->Cys (Y) [Unimod]\n+NA-LNO2 (C) [Unimod]\n+NA-LNO2 (H) [Unimod]\n+NA-OA-NO2 (C) [Unimod]\n+NA-OA-NO2 (H) [Unimod]\n+ICPL:2H(4) (N-term) [Unimod]\n+ICPL:2H(4) (N-term) [Unimod]\n+ICPL:2H(4) (K) [Unimod]\n+iTRAQ8plex (Y) [Unimod]\n+iTRAQ8plex (N-term) [Unimod]\n+iTRAQ8plex (K) [Unimod]\n+Label:13C(6)15N(1) (I) [Unimod]\n+Label:13C(6)15N(1) (L) [Unimod]\n+Label:2H(9)13C(6)15N(2) (K) [Unimod]\n+HNE-Delta:H(2)O (K) [Unimod]\n+HNE-Delta:H(2)O (H) [Unimod]\n+HNE-Delta:H(2)O (C) [Unimod]\n+4-ONE (K) [Unimod]\n+4-ONE (H) [Unimod]\n+4-ONE (C) [Unimod]\n+O-Dimethylphosphate (Y) [Unimod]\n+O-Dimethylphosphate (T) [Unimod]\n+O-Dimethylphosphate (S) [Unimod]\n+O-Methylphosphate (Y) [Unimod]\n+O-Methylphosphate (T) [Unimod]\n+O-Methylphosphate (S) [Unimod]\n+O-Diethylphosphate (Y) [Unimod]\n+O-Diethylphosphate (T) [Unimod]\n+O-Diethylphosphate (S) [Unimod]\n+O-Ethylphosphate (Y) [Unimod]\n+O-Ethylphosphate (T) [Unimod]\n+O-Ethylphosphate (S) [Unimod]\n+O-pinacolylmethylphosphonate (Y) [Unimod]\n+O-pinacolylmethylphosphonate (T) [Unimod]\n+O-pinacolylmethylphosphonate (S) [Unimod]\n+Methylphosphonate (Y) [Unimod]\n+Methylphosphonate (T) [Unimod]\n+Methylphosphonate (S) [Unimod]\n+O-Isopropylmethylphosphonate (Y) [Unimod]\n+O-Isopropylmethylphosphonate (T) [Unimod]\n+O-Isopropylmethylphosphonate (S) [Unimod]\n+iTRAQ8plex:13C(6)15N(2) (Y) [Unimod]\n+iTRAQ8plex:13C(6)15N(2) (N-term) [Unimod]\n+iTRAQ8plex:13C(6)15N(2) (K) [Unimod]\n+DTT_ST (S) [Unimod]\n+DTT_ST (T) [Unimod]\n+Ethanolamine (D) [Unimod]\n+Ethanolamine (C-term) [Unimod]\n+Ethanolamine (E) [Unimod]\n+TMT6plex (K) [Unimod]\n+TMT6plex (N-term) [Unimod]\n+DTT_C (C) [Unimod]\n+TMT2plex (N-term) [Unimod]\n+TMT2plex (K) [Unimod]\n+TMT (N-term) [Unimod]\n+TMT (K) [Unimod]\n+ExacTagThiol (C) [Unimod]\n+ExacTagAmine (K) [Unimod]\n+NO_SMX_SEMD (C) [Unimod]\n+4-ONE+Delta:H(-2)O(-1) (K) [Unimod]\n+4-ONE+Delta:H(-2)O(-1) (H) [Unimod]\n+4-ONE+Delta:H(-2)O(-1) (C) [Unimod]\n+NO_SMX_SMCT (C) [Unimod]\n+NO_SMX_SIMD (C) [Unimod]\n+Malonyl (C) [Unimod]\n+Malonyl (S) [Unimod]\n+3sulfo (N-term) [Unimod]\n+trifluoro (L) [Unimod]\n+TNBS (N-term) [Unimod]\n+TNBS (K) [Unimod]\n+Biotin-phenacyl (C) [Unimod]\n+Biotin-phenacyl (H) [Unimod]\n+Biotin-phenacyl (S) [Unimod]\n+DTT_C:2H(6) (C) [Unimod]\n+lapachenole (C) [Unimod]\n+Label:13C(5) (P) [Unimod]\n+maleimide (K) [Unimod]\n+maleimide (C) [Unimod]\n+DTT_ST:2H(6) (T) [Unimod]\n+DTT_ST:2H(6) (S) [Unimod]\n+Met-loss (M) [Unimod]\n+Met-loss+Acetyl (M) [Unimod]\n+Menadione-HQ (K) [Unimod]\n+Menadione-HQ (C) [Unimod]\n+Carboxymethyl:13C(2) (C) [Unimod]\n+NEM:2H(5) (C) [Unimod]\n+Gly-loss+Amide (G) [Unimod]\n+TMPP-Ac (N-term) [Unimod]\n+Label:13C(6)+GlyGly (K) [Unimod]\n+Arg->Npo (R) [Unimod]\n+Label:2H(4)+Acetyl (K) [Unimod]\n+Pentylamine (Q) [Unimod]\n+PentylamineBiotin (Q) [Unimod]\n+Dihydroxyimidazolidine (R) [Unimod]\n+DFDNB (Q) [Unimod]\n+DFDNB (N) [Unimod]\n+DFDNB (R) [Unimod]\n+DFDNB (K) [Unimod]\n+Cy3b-maleimide (C) [Unimod]\n+AEC-MAEC:2H(4) (S) [Unimod]\n+AEC-MAEC:2H(4) (T) [Unimod]\n+BMOE (C) [Unimod]\n+Biotin-PEO4-hydrazide (C-term) [Unimod]\n+Label:13C(6)+Acetyl (K) [Unimod]\n+Label:13C(6)15N(2)+Acetyl (K) [Unimod]\n+EQIGG (K) [Unimod]\n+cGMP (C) [Unimod]\n+cGMP+RMP-loss (C) [Unimod]\n+Arg2PG (R) [Unimod]\n+Label:2H(4)+GlyGly (K) [Unimod]\n+Label:13C(8)15N(2) (R) [Unimod]\n+Label:13C(1)2H(3) (M) [Unimod]\n+ZGB (K) [Unimod]\n+ZGB (N-term) [Unimod]\n+MG-H1 (R) [Unimod]\n+G-H1 (R) [Unimod]\n+Label:13C(6)15N(2)+GlyGly (K) [Unimod]\n+ICPL:13C(6)2H(4) (N-term) [Unimod]\n+ICPL:13C(6)2H(4) (K) [Unimod]\n+ICPL:13C(6)2H(4) (N-term) [Unimod]\n+QQQTGG (K) [Unimod]\n+QEQTGG (K) [Unimod]\n+Bodipy (C) [Unimod]\n' |
| b |
| diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc.sample Fri May 10 17:22:51 2013 -0400 |
| b |
| @@ -0,0 +1,396 @@ +Oxidation (M) +Acetyl (Protein N-term) +Acetyl (K) +Ala->Arg +Ala->Asn +Ala->Asp +Ala->CamCys +Ala->Cys +Ala->Gln +Ala->Glu +Ala->Gly +Ala->His +Ala->Lys +Ala->Met +Ala->Phe +Ala->Pro +Ala->Ser +Ala->Thr +Ala->Trp +Ala->Tyr +Ala->Val +Ala->Xle +Arg->Ala +Arg->Asn +Arg->Asp +Arg->CamCys +Arg->Cys +Arg->Gln +Arg->Glu +Arg->Gly +Arg->His +Arg->Lys +Arg->Met +Arg->Phe +Arg->Pro +Arg->Ser +Arg->Thr +Arg->Trp +Arg->Tyr +Arg->Val +Arg->Xle +Asn->Ala +Asn->Arg +Asn->Asp +Asn->CamCys +Asn->Cys +Asn->Gln +Asn->Glu +Asn->Gly +Asn->His +Asn->Lys +Asn->Met +Asn->Phe +Asn->Pro +Asn->Ser +Asn->Thr +Asn->Trp +Asn->Tyr +Asn->Val +Asn->Xle +Asp->Ala +Asp->Arg +Asp->Asn +Asp->CamCys +Asp->Cys +Asp->Gln +Asp->Glu +Asp->Gly +Asp->His +Asp->Lys +Asp->Met +Asp->Phe +Asp->Pro +Asp->Ser +Asp->Thr +Asp->Trp +Asp->Tyr +Asp->Val +Asp->Xle +CamCys->Ala +CamCys->Arg +CamCys->Asn +CamCys->Asp +CamCys->Gln +CamCys->Glu +CamCys->Gly +CamCys->His +CamCys->Lys +CamCys->Met +CamCys->Phe +CamCys->Pro +CamCys->Ser +CamCys->Thr +CamCys->Trp +CamCys->Tyr +CamCys->Val +CamCys->Xle +Carbamidomethyl (C) +Cys->Ala +Cys->Arg +Cys->Asn +Cys->Asp +Cys->Gln +Cys->Glu +Cys->Gly +Cys->His +Cys->Lys +Cys->Met +Cys->Phe +Cys->Pro +Cys->Ser +Cys->Thr +Cys->Trp +Cys->Tyr +Cys->Val +Cys->Xle +Deamidation (N) +Deamidation (NQ) +Deamidation 18O (N) +Dimethyl (KR) +Gln->Ala +Gln->Arg +Gln->Asn +Gln->Asp +Gln->CamCys +Gln->Cys +Gln->Glu +Gln->Gly +Gln->His +Gln->Lys +Gln->Met +Gln->Phe +Gln->Pro +Gln->pyro-Glu +Gln->Ser +Gln->Thr +Gln->Trp +Gln->Tyr +Gln->Val +Gln->Xle +Glu->Ala +Glu->Arg +Glu->Asn +Glu->Asp +Glu->CamCys +Glu->Cys +Glu->Gln +Glu->Gly +Glu->His +Glu->Lys +Glu->Met +Glu->Phe +Glu->Pro +Glu->pyro-Glu +Glu->Ser +Glu->Thr +Glu->Trp +Glu->Tyr +Glu->Val +Glu->Xle +Gly->Ala +Gly->Arg +Gly->Asn +Gly->Asp +Gly->CamCys +Gly->Cys +Gly->Gln +Gly->Glu +Gly->His +Gly->Lys +Gly->Met +Gly->Phe +Gly->Pro +Gly->Ser +Gly->Thr +Gly->Trp +Gly->Tyr +Gly->Val +Gly->Xle +GlyGly (K) +His->Ala +His->Arg +His->Asn +His->Asp +His->CamCys +His->Cys +His->Gln +His->Glu +His->Gly +His->Lys +His->Met +His->Phe +His->Pro +His->Ser +His->Thr +His->Trp +His->Tyr +His->Val +His->Xle +Lys->Ala +Lys->Arg +Lys->Asn +Lys->Asp +Lys->CamCys +Lys->Cys +Lys->Gln +Lys->Glu +Lys->Gly +Lys->His +Lys->Met +Lys->Phe +Lys->Pro +Lys->Ser +Lys->Thr +Lys->Trp +Lys->Tyr +Lys->Val +Lys->Xle +Met->Ala +Met->Arg +Met->Asn +Met->Asp +Met->CamCys +Met->Cys +Met->Gln +Met->Glu +Met->Gly +Met->His +Met->Lys +Met->Phe +Met->Pro +Met->Ser +Met->Thr +Met->Trp +Met->Tyr +Met->Val +Met->Xle +Methyl (KR) +OHexNAc +Phe->Ala +Phe->Arg +Phe->Asn +Phe->Asp +Phe->CamCys +Phe->Cys +Phe->Gln +Phe->Glu +Phe->Gly +Phe->His +Phe->Lys +Phe->Met +Phe->Pro +Phe->Ser +Phe->Thr +Phe->Trp +Phe->Tyr +Phe->Val +Phe->Xle +Phospho (STY) +Pro->Ala +Pro->Arg +Pro->Asn +Pro->Asp +Pro->CamCys +Pro->Cys +Pro->Gln +Pro->Glu +Pro->Gly +Pro->His +Pro->Lys +Pro->Met +Pro->Phe +Pro->Ser +Pro->Thr +Pro->Trp +Pro->Tyr +Pro->Val +Pro->Xle +Pro5 +Pro6 +QQTGG (K) +Ser->Ala +Ser->Arg +Ser->Asn +Ser->Asp +Ser->CamCys +Ser->Cys +Ser->Gln +Ser->Glu +Ser->Gly +Ser->His +Ser->Lys +Ser->Met +Ser->Phe +Ser->Pro +Ser->Thr +Ser->Trp +Ser->Tyr +Ser->Val +Ser->Xle +Thr->Ala +Thr->Arg +Thr->Asn +Thr->Asp +Thr->CamCys +Thr->Cys +Thr->Gln +Thr->Glu +Thr->Gly +Thr->His +Thr->Lys +Thr->Met +Thr->Phe +Thr->Pro +Thr->Ser +Thr->Trp +Thr->Tyr +Thr->Val +Thr->Xle +Trimethyl (K) +Trp->Ala +Trp->Arg +Trp->Asn +Trp->Asp +Trp->CamCys +Trp->Cys +Trp->Gln +Trp->Glu +Trp->Gly +Trp->His +Trp->Lys +Trp->Met +Trp->Phe +Trp->Pro +Trp->Ser +Trp->Thr +Trp->Tyr +Trp->Val +Trp->Xle +Tyr->Ala +Tyr->Arg +Tyr->Asn +Tyr->Asp +Tyr->CamCys +Tyr->Cys +Tyr->Gln +Tyr->Glu +Tyr->Gly +Tyr->His +Tyr->Lys +Tyr->Met +Tyr->Phe +Tyr->Pro +Tyr->Ser +Tyr->Thr +Tyr->Trp +Tyr->Val +Tyr->Xle +Val->Ala +Val->Arg +Val->Asn +Val->Asp +Val->CamCys +Val->Cys +Val->Gln +Val->Glu +Val->Gly +Val->His +Val->Lys +Val->Met +Val->Phe +Val->Pro +Val->Ser +Val->Thr +Val->Trp +Val->Tyr +Val->Xle +Xle->Ala +Xle->Arg +Xle->Asn +Xle->Asp +Xle->CamCys +Xle->Cys +Xle->Gln +Xle->Glu +Xle->Gly +Xle->His +Xle->Lys +Xle->Met +Xle->Phe +Xle->Pro +Xle->Ser +Xle->Thr +Xle->Trp +Xle->Tyr +Xle->Val |
| b |
| diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc.sample.default --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc.sample.default Fri May 10 17:22:51 2013 -0400 |
| b |
| @@ -0,0 +1,396 @@ +Oxidation (M) +Acetyl (Protein N-term) +Acetyl (K) +Ala->Arg +Ala->Asn +Ala->Asp +Ala->CamCys +Ala->Cys +Ala->Gln +Ala->Glu +Ala->Gly +Ala->His +Ala->Lys +Ala->Met +Ala->Phe +Ala->Pro +Ala->Ser +Ala->Thr +Ala->Trp +Ala->Tyr +Ala->Val +Ala->Xle +Arg->Ala +Arg->Asn +Arg->Asp +Arg->CamCys +Arg->Cys +Arg->Gln +Arg->Glu +Arg->Gly +Arg->His +Arg->Lys +Arg->Met +Arg->Phe +Arg->Pro +Arg->Ser +Arg->Thr +Arg->Trp +Arg->Tyr +Arg->Val +Arg->Xle +Asn->Ala +Asn->Arg +Asn->Asp +Asn->CamCys +Asn->Cys +Asn->Gln +Asn->Glu +Asn->Gly +Asn->His +Asn->Lys +Asn->Met +Asn->Phe +Asn->Pro +Asn->Ser +Asn->Thr +Asn->Trp +Asn->Tyr +Asn->Val +Asn->Xle +Asp->Ala +Asp->Arg +Asp->Asn +Asp->CamCys +Asp->Cys +Asp->Gln +Asp->Glu +Asp->Gly +Asp->His +Asp->Lys +Asp->Met +Asp->Phe +Asp->Pro +Asp->Ser +Asp->Thr +Asp->Trp +Asp->Tyr +Asp->Val +Asp->Xle +CamCys->Ala +CamCys->Arg +CamCys->Asn +CamCys->Asp +CamCys->Gln +CamCys->Glu +CamCys->Gly +CamCys->His +CamCys->Lys +CamCys->Met +CamCys->Phe +CamCys->Pro +CamCys->Ser +CamCys->Thr +CamCys->Trp +CamCys->Tyr +CamCys->Val +CamCys->Xle +Carbamidomethyl (C) +Cys->Ala +Cys->Arg +Cys->Asn +Cys->Asp +Cys->Gln +Cys->Glu +Cys->Gly +Cys->His +Cys->Lys +Cys->Met +Cys->Phe +Cys->Pro +Cys->Ser +Cys->Thr +Cys->Trp +Cys->Tyr +Cys->Val +Cys->Xle +Deamidation (N) +Deamidation (NQ) +Deamidation 18O (N) +Dimethyl (KR) +Gln->Ala +Gln->Arg +Gln->Asn +Gln->Asp +Gln->CamCys +Gln->Cys +Gln->Glu +Gln->Gly +Gln->His +Gln->Lys +Gln->Met +Gln->Phe +Gln->Pro +Gln->pyro-Glu +Gln->Ser +Gln->Thr +Gln->Trp +Gln->Tyr +Gln->Val +Gln->Xle +Glu->Ala +Glu->Arg +Glu->Asn +Glu->Asp +Glu->CamCys +Glu->Cys +Glu->Gln +Glu->Gly +Glu->His +Glu->Lys +Glu->Met +Glu->Phe +Glu->Pro +Glu->pyro-Glu +Glu->Ser +Glu->Thr +Glu->Trp +Glu->Tyr +Glu->Val +Glu->Xle +Gly->Ala +Gly->Arg +Gly->Asn +Gly->Asp +Gly->CamCys +Gly->Cys +Gly->Gln +Gly->Glu +Gly->His +Gly->Lys +Gly->Met +Gly->Phe +Gly->Pro +Gly->Ser +Gly->Thr +Gly->Trp +Gly->Tyr +Gly->Val +Gly->Xle +GlyGly (K) +His->Ala +His->Arg +His->Asn +His->Asp +His->CamCys +His->Cys +His->Gln +His->Glu +His->Gly +His->Lys +His->Met +His->Phe +His->Pro +His->Ser +His->Thr +His->Trp +His->Tyr +His->Val +His->Xle +Lys->Ala +Lys->Arg +Lys->Asn +Lys->Asp +Lys->CamCys +Lys->Cys +Lys->Gln +Lys->Glu +Lys->Gly +Lys->His +Lys->Met +Lys->Phe +Lys->Pro +Lys->Ser +Lys->Thr +Lys->Trp +Lys->Tyr +Lys->Val +Lys->Xle +Met->Ala +Met->Arg +Met->Asn +Met->Asp +Met->CamCys +Met->Cys +Met->Gln +Met->Glu +Met->Gly +Met->His +Met->Lys +Met->Phe +Met->Pro +Met->Ser +Met->Thr +Met->Trp +Met->Tyr +Met->Val +Met->Xle +Methyl (KR) +OHexNAc +Phe->Ala +Phe->Arg +Phe->Asn +Phe->Asp +Phe->CamCys +Phe->Cys +Phe->Gln +Phe->Glu +Phe->Gly +Phe->His +Phe->Lys +Phe->Met +Phe->Pro +Phe->Ser +Phe->Thr +Phe->Trp +Phe->Tyr +Phe->Val +Phe->Xle +Phospho (STY) +Pro->Ala +Pro->Arg +Pro->Asn +Pro->Asp +Pro->CamCys +Pro->Cys +Pro->Gln +Pro->Glu +Pro->Gly +Pro->His +Pro->Lys +Pro->Met +Pro->Phe +Pro->Ser +Pro->Thr +Pro->Trp +Pro->Tyr +Pro->Val +Pro->Xle +Pro5 +Pro6 +QQTGG (K) +Ser->Ala +Ser->Arg +Ser->Asn +Ser->Asp +Ser->CamCys +Ser->Cys +Ser->Gln +Ser->Glu +Ser->Gly +Ser->His +Ser->Lys +Ser->Met +Ser->Phe +Ser->Pro +Ser->Thr +Ser->Trp +Ser->Tyr +Ser->Val +Ser->Xle +Thr->Ala +Thr->Arg +Thr->Asn +Thr->Asp +Thr->CamCys +Thr->Cys +Thr->Gln +Thr->Glu +Thr->Gly +Thr->His +Thr->Lys +Thr->Met +Thr->Phe +Thr->Pro +Thr->Ser +Thr->Trp +Thr->Tyr +Thr->Val +Thr->Xle +Trimethyl (K) +Trp->Ala +Trp->Arg +Trp->Asn +Trp->Asp +Trp->CamCys +Trp->Cys +Trp->Gln +Trp->Glu +Trp->Gly +Trp->His +Trp->Lys +Trp->Met +Trp->Phe +Trp->Pro +Trp->Ser +Trp->Thr +Trp->Tyr +Trp->Val +Trp->Xle +Tyr->Ala +Tyr->Arg +Tyr->Asn +Tyr->Asp +Tyr->CamCys +Tyr->Cys +Tyr->Gln +Tyr->Glu +Tyr->Gly +Tyr->His +Tyr->Lys +Tyr->Met +Tyr->Phe +Tyr->Pro +Tyr->Ser +Tyr->Thr +Tyr->Trp +Tyr->Val +Tyr->Xle +Val->Ala +Val->Arg +Val->Asn +Val->Asp +Val->CamCys +Val->Cys +Val->Gln +Val->Glu +Val->Gly +Val->His +Val->Lys +Val->Met +Val->Phe +Val->Pro +Val->Ser +Val->Thr +Val->Trp +Val->Tyr +Val->Xle +Xle->Ala +Xle->Arg +Xle->Asn +Xle->Asp +Xle->CamCys +Xle->Cys +Xle->Gln +Xle->Glu +Xle->Gly +Xle->His +Xle->Lys +Xle->Met +Xle->Phe +Xle->Pro +Xle->Ser +Xle->Thr +Xle->Trp +Xle->Tyr +Xle->Val |
| b |
| diff -r 000000000000 -r d4b6c9eae635 maxquant_mods.loc.sample.extended --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_mods.loc.sample.extended Fri May 10 17:22:51 2013 -0400 |
| [ |
| b'@@ -0,0 +1,1308 @@\n+Acetyl (K)\n+Acetyl (Protein N-term)\n+Carbamidomethyl (C)\n+Oxidation (M)\n+Phospho (STY)\n+Arg6\n+Arg10\n+Lys4\n+Lys6\n+Lys8\n+GlyGly (K)\n+Methyl (KR)\n+Dimethyl (KR)\n+Trimethyl (K)\n+Pro5\n+Pro6\n+Glu->pyro-Glu\n+Gln->pyro-Glu\n+OHexNAc\n+DimethLys0\n+DimethNter0\n+DimethLys4\n+DimethNter4\n+DimethLys8\n+DimethNter8\n+18O\n+ICAT-0\n+ICAT-9\n+ICPL-Lys0\n+ICPL-Nter0\n+ICPL-Lys4\n+ICPL-Nter4\n+ICPL-Lys6\n+ICPL-Nter6\n+ICPL-Lys10\n+ICPL-Nter10\n+mTRAQ-Lys0\n+mTRAQ-Nter0\n+mTRAQ-Lys4\n+mTRAQ-Nter4\n+mTRAQ-Lys8\n+mTRAQ-Nter8\n+DimethLys2\n+DimethNter2\n+DimethLys6\n+DimethNter6\n+QQTGG (K)\n+Deamidation (N)\n+Deamidation 18O (N)\n+iTRAQ4plex-Nter114\n+iTRAQ4plex-Nter115\n+iTRAQ4plex-Nter116\n+iTRAQ4plex-Nter117\n+iTRAQ4plex-Lys114\n+iTRAQ4plex-Lys115\n+iTRAQ4plex-Lys116\n+iTRAQ4plex-Lys117\n+iTRAQ8plex-Nter113\n+iTRAQ8plex-Nter114\n+iTRAQ8plex-Nter115\n+iTRAQ8plex-Nter116\n+iTRAQ8plex-Nter117\n+iTRAQ8plex-Nter118\n+iTRAQ8plex-Nter119\n+iTRAQ8plex-Nter121\n+iTRAQ8plex-Lys113\n+iTRAQ8plex-Lys114\n+iTRAQ8plex-Lys115\n+iTRAQ8plex-Lys116\n+iTRAQ8plex-Lys117\n+iTRAQ8plex-Lys118\n+iTRAQ8plex-Lys119\n+iTRAQ8plex-Lys121\n+TMT2plex-Nter126\n+TMT2plex-Nter127\n+TMT2plex-Lys126\n+TMT2plex-Lys127\n+TMT6plex-Nter126\n+TMT6plex-Nter127\n+TMT6plex-Nter128\n+TMT6plex-Nter129\n+TMT6plex-Nter130\n+TMT6plex-Nter131\n+TMT6plex-Lys126\n+TMT6plex-Lys127\n+TMT6plex-Lys128\n+TMT6plex-Lys129\n+TMT6plex-Lys130\n+TMT6plex-Lys131\n+Deamidation (NQ)\n+Ala->Arg\n+Ala->Asn\n+Ala->Asp\n+Ala->Cys\n+Ala->Gln\n+Ala->Glu\n+Ala->Gly\n+Ala->His\n+Ala->Xle\n+Ala->Lys\n+Ala->Met\n+Ala->Phe\n+Ala->Pro\n+Ala->Ser\n+Ala->Thr\n+Ala->Trp\n+Ala->Tyr\n+Ala->Val\n+Arg->Ala\n+Arg->Asn\n+Arg->Asp\n+Arg->Cys\n+Arg->Gln\n+Arg->Glu\n+Arg->Gly\n+Arg->His\n+Arg->Lys\n+Arg->Met\n+Arg->Phe\n+Arg->Pro\n+Arg->Ser\n+Arg->Thr\n+Arg->Trp\n+Arg->Tyr\n+Arg->Val\n+Arg->Xle\n+Asn->Ala\n+Asn->Arg\n+Asn->Asp\n+Asn->Cys\n+Asn->Gln\n+Asn->Glu\n+Asn->Gly\n+Asn->His\n+Asn->Lys\n+Asn->Met\n+Asn->Phe\n+Asn->Pro\n+Asn->Ser\n+Asn->Thr\n+Asn->Trp\n+Asn->Tyr\n+Asn->Val\n+Asn->Xle\n+Asp->Ala\n+Asp->Arg\n+Asp->Asn\n+Asp->Cys\n+Asp->Gln\n+Asp->Glu\n+Asp->Gly\n+Asp->His\n+Asp->Lys\n+Asp->Met\n+Asp->Phe\n+Asp->Pro\n+Asp->Ser\n+Asp->Thr\n+Asp->Trp\n+Asp->Tyr\n+Asp->Val\n+Asp->Xle\n+Cys->Ala\n+Cys->Arg\n+Cys->Asn\n+Cys->Asp\n+Cys->Gln\n+Cys->Glu\n+Cys->Gly\n+Cys->His\n+Cys->Lys\n+Cys->Met\n+Cys->Phe\n+Cys->Pro\n+Cys->Ser\n+Cys->Thr\n+Cys->Trp\n+Cys->Tyr\n+Cys->Val\n+Cys->Xle\n+Gln->Ala\n+Gln->Arg\n+Gln->Asn\n+Gln->Asp\n+Gln->Cys\n+Gln->Glu\n+Gln->Gly\n+Gln->His\n+Gln->Lys\n+Gln->Met\n+Gln->Phe\n+Gln->Pro\n+Gln->Ser\n+Gln->Thr\n+Gln->Trp\n+Gln->Tyr\n+Gln->Val\n+Gln->Xle\n+Glu->Ala\n+Glu->Arg\n+Glu->Asn\n+Glu->Asp\n+Glu->Cys\n+Glu->Gln\n+Glu->Gly\n+Glu->His\n+Glu->Lys\n+Glu->Met\n+Glu->Phe\n+Glu->Pro\n+Glu->Ser\n+Glu->Thr\n+Glu->Trp\n+Glu->Tyr\n+Glu->Val\n+Glu->Xle\n+Gly->Ala\n+Gly->Arg\n+Gly->Asn\n+Gly->Asp\n+Gly->Cys\n+Gly->Gln\n+Gly->Glu\n+Gly->His\n+Gly->Lys\n+Gly->Met\n+Gly->Phe\n+Gly->Pro\n+Gly->Ser\n+Gly->Thr\n+Gly->Trp\n+Gly->Tyr\n+Gly->Val\n+Gly->Xle\n+His->Ala\n+His->Arg\n+His->Asn\n+His->Asp\n+His->Cys\n+His->Gln\n+His->Glu\n+His->Gly\n+His->Lys\n+His->Met\n+His->Phe\n+His->Pro\n+His->Ser\n+His->Thr\n+His->Trp\n+His->Tyr\n+His->Val\n+His->Xle\n+Lys->Ala\n+Lys->Arg\n+Lys->Asn\n+Lys->Asp\n+Lys->Cys\n+Lys->Gln\n+Lys->Glu\n+Lys->Gly\n+Lys->His\n+Lys->Met\n+Lys->Phe\n+Lys->Pro\n+Lys->Ser\n+Lys->Thr\n+Lys->Trp\n+Lys->Tyr\n+Lys->Val\n+Lys->Xle\n+Met->Ala\n+Met->Arg\n+Met->Asn\n+Met->Asp\n+Met->Cys\n+Met->Gln\n+Met->Glu\n+Met->Gly\n+Met->His\n+Met->Lys\n+Met->Phe\n+Met->Pro\n+Met->Ser\n+Met->Thr\n+Met->Trp\n+Met->Tyr\n+Met->Val\n+Met->Xle\n+Phe->Ala\n+Phe->Arg\n+Phe->Asn\n+Phe->Asp\n+Phe->Cys\n+Phe->Gln\n+Phe->Glu\n+Phe->Gly\n+Phe->His\n+Phe->Lys\n+Phe->Met\n+Phe->Pro\n+Phe->Ser\n+Phe->Thr\n+Phe->Trp\n+Phe->Tyr\n+Phe->Val\n+Phe->Xle\n+Pro->Ala\n+Pro->Arg\n+Pro->Asn\n+Pro->Asp\n+Pro->Cys\n+Pro->Gln\n+Pro->Glu\n+Pro->Gly\n+Pro->His\n+Pro->Lys\n+Pro->Met\n+Pro->Phe\n+Pro->Ser\n+Pro->Thr\n+Pro->Trp\n+Pro->Tyr\n+Pro->Val\n+Pro->Xle\n+Ser->Ala\n+Ser->Arg\n+Ser->Asn\n+Ser->Asp\n+Ser->Cys\n+Ser->Gln\n+Ser->Glu\n+Ser->Gly\n+Ser->His\n+Ser->Lys\n+Ser->Met\n+Ser->Phe\n+Ser->Pro\n+Ser->Thr\n+Ser->Trp\n+Ser->Tyr\n+Ser->Val\n+Ser->Xle\n+Thr->Ala\n+Thr->Arg\n+Thr->Asn\n+Thr->Asp\n+Thr->Cys\n+Thr->Gln\n+Thr->Glu\n+Thr->Gly\n+Thr->His\n+Thr->Lys\n+Thr-'..b'r->Pro (T) [Unimod]\n+Thr->Met (T) [Unimod]\n+Thr->Ile (T) [Unimod]\n+Thr->Arg (T) [Unimod]\n+Val->Phe (V) [Unimod]\n+Val->Ala (V) [Unimod]\n+Val->Glu (V) [Unimod]\n+Val->Met (V) [Unimod]\n+Val->Asp (V) [Unimod]\n+Val->Ile (V) [Unimod]\n+Val->Gly (V) [Unimod]\n+Trp->Ser (W) [Unimod]\n+Trp->Cys (W) [Unimod]\n+Trp->Arg (W) [Unimod]\n+Trp->Gly (W) [Unimod]\n+Trp->Leu (W) [Unimod]\n+Tyr->Phe (Y) [Unimod]\n+Tyr->Ser (Y) [Unimod]\n+Tyr->Asn (Y) [Unimod]\n+Tyr->His (Y) [Unimod]\n+Tyr->Asp (Y) [Unimod]\n+Tyr->Cys (Y) [Unimod]\n+NA-LNO2 (C) [Unimod]\n+NA-LNO2 (H) [Unimod]\n+NA-OA-NO2 (C) [Unimod]\n+NA-OA-NO2 (H) [Unimod]\n+ICPL:2H(4) (N-term) [Unimod]\n+ICPL:2H(4) (N-term) [Unimod]\n+ICPL:2H(4) (K) [Unimod]\n+iTRAQ8plex (Y) [Unimod]\n+iTRAQ8plex (N-term) [Unimod]\n+iTRAQ8plex (K) [Unimod]\n+Label:13C(6)15N(1) (I) [Unimod]\n+Label:13C(6)15N(1) (L) [Unimod]\n+Label:2H(9)13C(6)15N(2) (K) [Unimod]\n+HNE-Delta:H(2)O (K) [Unimod]\n+HNE-Delta:H(2)O (H) [Unimod]\n+HNE-Delta:H(2)O (C) [Unimod]\n+4-ONE (K) [Unimod]\n+4-ONE (H) [Unimod]\n+4-ONE (C) [Unimod]\n+O-Dimethylphosphate (Y) [Unimod]\n+O-Dimethylphosphate (T) [Unimod]\n+O-Dimethylphosphate (S) [Unimod]\n+O-Methylphosphate (Y) [Unimod]\n+O-Methylphosphate (T) [Unimod]\n+O-Methylphosphate (S) [Unimod]\n+O-Diethylphosphate (Y) [Unimod]\n+O-Diethylphosphate (T) [Unimod]\n+O-Diethylphosphate (S) [Unimod]\n+O-Ethylphosphate (Y) [Unimod]\n+O-Ethylphosphate (T) [Unimod]\n+O-Ethylphosphate (S) [Unimod]\n+O-pinacolylmethylphosphonate (Y) [Unimod]\n+O-pinacolylmethylphosphonate (T) [Unimod]\n+O-pinacolylmethylphosphonate (S) [Unimod]\n+Methylphosphonate (Y) [Unimod]\n+Methylphosphonate (T) [Unimod]\n+Methylphosphonate (S) [Unimod]\n+O-Isopropylmethylphosphonate (Y) [Unimod]\n+O-Isopropylmethylphosphonate (T) [Unimod]\n+O-Isopropylmethylphosphonate (S) [Unimod]\n+iTRAQ8plex:13C(6)15N(2) (Y) [Unimod]\n+iTRAQ8plex:13C(6)15N(2) (N-term) [Unimod]\n+iTRAQ8plex:13C(6)15N(2) (K) [Unimod]\n+DTT_ST (S) [Unimod]\n+DTT_ST (T) [Unimod]\n+Ethanolamine (D) [Unimod]\n+Ethanolamine (C-term) [Unimod]\n+Ethanolamine (E) [Unimod]\n+TMT6plex (K) [Unimod]\n+TMT6plex (N-term) [Unimod]\n+DTT_C (C) [Unimod]\n+TMT2plex (N-term) [Unimod]\n+TMT2plex (K) [Unimod]\n+TMT (N-term) [Unimod]\n+TMT (K) [Unimod]\n+ExacTagThiol (C) [Unimod]\n+ExacTagAmine (K) [Unimod]\n+NO_SMX_SEMD (C) [Unimod]\n+4-ONE+Delta:H(-2)O(-1) (K) [Unimod]\n+4-ONE+Delta:H(-2)O(-1) (H) [Unimod]\n+4-ONE+Delta:H(-2)O(-1) (C) [Unimod]\n+NO_SMX_SMCT (C) [Unimod]\n+NO_SMX_SIMD (C) [Unimod]\n+Malonyl (C) [Unimod]\n+Malonyl (S) [Unimod]\n+3sulfo (N-term) [Unimod]\n+trifluoro (L) [Unimod]\n+TNBS (N-term) [Unimod]\n+TNBS (K) [Unimod]\n+Biotin-phenacyl (C) [Unimod]\n+Biotin-phenacyl (H) [Unimod]\n+Biotin-phenacyl (S) [Unimod]\n+DTT_C:2H(6) (C) [Unimod]\n+lapachenole (C) [Unimod]\n+Label:13C(5) (P) [Unimod]\n+maleimide (K) [Unimod]\n+maleimide (C) [Unimod]\n+DTT_ST:2H(6) (T) [Unimod]\n+DTT_ST:2H(6) (S) [Unimod]\n+Met-loss (M) [Unimod]\n+Met-loss+Acetyl (M) [Unimod]\n+Menadione-HQ (K) [Unimod]\n+Menadione-HQ (C) [Unimod]\n+Carboxymethyl:13C(2) (C) [Unimod]\n+NEM:2H(5) (C) [Unimod]\n+Gly-loss+Amide (G) [Unimod]\n+TMPP-Ac (N-term) [Unimod]\n+Label:13C(6)+GlyGly (K) [Unimod]\n+Arg->Npo (R) [Unimod]\n+Label:2H(4)+Acetyl (K) [Unimod]\n+Pentylamine (Q) [Unimod]\n+PentylamineBiotin (Q) [Unimod]\n+Dihydroxyimidazolidine (R) [Unimod]\n+DFDNB (Q) [Unimod]\n+DFDNB (N) [Unimod]\n+DFDNB (R) [Unimod]\n+DFDNB (K) [Unimod]\n+Cy3b-maleimide (C) [Unimod]\n+AEC-MAEC:2H(4) (S) [Unimod]\n+AEC-MAEC:2H(4) (T) [Unimod]\n+BMOE (C) [Unimod]\n+Biotin-PEO4-hydrazide (C-term) [Unimod]\n+Label:13C(6)+Acetyl (K) [Unimod]\n+Label:13C(6)15N(2)+Acetyl (K) [Unimod]\n+EQIGG (K) [Unimod]\n+cGMP (C) [Unimod]\n+cGMP+RMP-loss (C) [Unimod]\n+Arg2PG (R) [Unimod]\n+Label:2H(4)+GlyGly (K) [Unimod]\n+Label:13C(8)15N(2) (R) [Unimod]\n+Label:13C(1)2H(3) (M) [Unimod]\n+ZGB (K) [Unimod]\n+ZGB (N-term) [Unimod]\n+MG-H1 (R) [Unimod]\n+G-H1 (R) [Unimod]\n+Label:13C(6)15N(2)+GlyGly (K) [Unimod]\n+ICPL:13C(6)2H(4) (N-term) [Unimod]\n+ICPL:13C(6)2H(4) (K) [Unimod]\n+ICPL:13C(6)2H(4) (N-term) [Unimod]\n+QQQTGG (K) [Unimod]\n+QEQTGG (K) [Unimod]\n+Bodipy (C) [Unimod]\n' |
| b |
| diff -r 000000000000 -r d4b6c9eae635 maxquant_proteases.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_proteases.loc Fri May 10 17:22:51 2013 -0400 |
| b |
| @@ -0,0 +1,27 @@ +Trypsin +Arg-C +Asp-N +Asp-N_ambic +Chymotrypsin +CNBr +CNBr+Trypsin +Formic_acid +Lys-C +Lys-C/P +PepsinA +Tryp-CNBr +TrypChymo +Trypsin/P +Trypsin/P+DP +V8-DE +V8-E +semiTrypsin +LysC+AspN +Lys-C/P+DP +Trypsin/P + Asp-N +Asp-C +Trypsin/P+Asp-C +SemiLys +SemiGluC +LysC/P+AspC +GluC |
| b |
| diff -r 000000000000 -r d4b6c9eae635 maxquant_proteases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_proteases.loc.sample Fri May 10 17:22:51 2013 -0400 |
| b |
| @@ -0,0 +1,27 @@ +Trypsin +Arg-C +Asp-N +Asp-N_ambic +Chymotrypsin +CNBr +CNBr+Trypsin +Formic_acid +Lys-C +Lys-C/P +PepsinA +Tryp-CNBr +TrypChymo +Trypsin/P +Trypsin/P+DP +V8-DE +V8-E +semiTrypsin +LysC+AspN +Lys-C/P+DP +Trypsin/P + Asp-N +Asp-C +Trypsin/P+Asp-C +SemiLys +SemiGluC +LysC/P+AspC +GluC |
| b |
| diff -r 000000000000 -r d4b6c9eae635 maxquant_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maxquant_wrapper.py Fri May 10 17:22:51 2013 -0400 |
| [ |
| b'@@ -0,0 +1,787 @@\n+#!/usr/bin/env python\n+import optparse\n+import os\n+import shutil\n+import sys\n+import tempfile\n+import subprocess\n+import logging\n+from string import Template\n+from xml.sax.saxutils import escape\n+import xml.etree.ElementTree as ET\n+\n+log = logging.getLogger(__name__)\n+\n+DEBUG = True\n+\n+working_directory = os.getcwd()\n+tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stderr\').name\n+tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix=\'.stdout\').name\n+\n+\n+def stop_err(msg):\n+ sys.stderr.write("%s\\n" % msg)\n+ sys.exit()\n+\n+\n+def read_stderr():\n+ stderr = \'\'\n+ if(os.path.exists(tmp_stderr_name)):\n+ with open(tmp_stderr_name, \'rb\') as tmp_stderr:\n+ buffsize = 1048576\n+ try:\n+ while True:\n+ stderr += tmp_stderr.read(buffsize)\n+ if not stderr or len(stderr) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ return stderr\n+\n+\n+def execute(command, stdin=None):\n+ try:\n+ with open(tmp_stderr_name, \'wb\') as tmp_stderr:\n+ with open(tmp_stdout_name, \'wb\') as tmp_stdout:\n+ proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)\n+ returncode = proc.wait()\n+ if returncode != 0:\n+ raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))\n+ finally:\n+ print open(tmp_stderr_name, "r").read(64000)\n+ print open(tmp_stdout_name, "r").read(64000)\n+\n+\n+def delete_file(path):\n+ if os.path.exists(path):\n+ try:\n+ os.remove(path)\n+ except:\n+ pass\n+\n+\n+def delete_directory(directory):\n+ if os.path.exists(directory):\n+ try:\n+ shutil.rmtree(directory)\n+ except:\n+ pass\n+\n+\n+def symlink(source, link_name):\n+ import platform\n+ if platform.system() == \'Windows\':\n+ try:\n+ import win32file\n+ win32file.CreateSymbolicLink(source, link_name, 1)\n+ except:\n+ shutil.copy(source, link_name)\n+ else:\n+ os.symlink(source, link_name)\n+\n+\n+def copy_to_working_directory(data_file, relative_path):\n+ if os.path.abspath(data_file) != os.path.abspath(relative_path):\n+ shutil.copy(data_file, relative_path)\n+ return relative_path\n+\n+\n+def __main__():\n+ run_script()\n+\n+\n+## Lock File Stuff\n+## http://www.evanfosmark.com/2009/01/cross-platform-file-locking-support-in-python/\n+import os\n+import time\n+import errno\n+\n+\n+class FileLockException(Exception):\n+ pass\n+\n+\n+class FileLock(object):\n+ """ A file locking mechanism that has context-manager support so\n+ you can use it in a with statement. This should be relatively cross\n+ compatible as it doesn\'t rely on msvcrt or fcntl for the locking.\n+ """\n+\n+ def __init__(self, file_name, timeout=10, delay=.05):\n+ """ Prepare the file locker. Specify the file to lock and optionally\n+ the maximum timeout and the delay between each attempt to lock.\n+ """\n+ self.is_locked = False\n+ self.lockfile = os.path.join(os.getcwd(), "%s.lock" % file_name)\n+ self.file_name = file_name\n+ self.timeout = timeout\n+ self.delay = delay\n+\n+ def acquire(self):\n+ """ Acquire the lock, if possible. If the lock is in use, it check again\n+ every `wait` seconds. It does this until it either gets the lock or\n+ exceeds `timeout` number of seconds, in which case it throws\n+ an exception.\n+ """\n+ start_time = time.time()\n+ while True:\n+ try:\n+ self.fd = os.open(self.lockfile, os.O_CREAT | os.O_EXCL | os.O_RDWR)\n+ break\n+ except OSError as e:\n+ if e.errno != errno.'..b'_option("--msms_connection", default="false")\n+ parser.add_option("--ibaq", default="false")\n+ parser.add_option("--msms_recalibration", default="false")\n+ parser.add_option("--ibaq_log_fit", default="true")\n+ parser.add_option("--razor_protein_fdr", default="true")\n+ parser.add_option("--calc_sequence_tags", default="false")\n+ parser.add_option("--de_novo_var_mods", default="true")\n+ parser.add_option("--mass_difference_search", default="false")\n+ parser.add_option("--min_pep_len", default="7")\n+ parser.add_option("--peptide_fdr", default="0.01")\n+ parser.add_option("--peptide_pep", default="1")\n+ parser.add_option("--protein_fdr", default="0.01")\n+ parser.add_option("--site_fdr", default="0.01")\n+ parser.add_option("--min_peptide_length_for_unspecific_search", default="8")\n+ parser.add_option("--max_peptide_length_for_unspecific_search", default="25")\n+ parser.add_option("--use_norm_ratios_for_occupancy", default="true")\n+ parser.add_option("--min_peptides", default="1")\n+ parser.add_option("--min_razor_peptides", default="1")\n+ parser.add_option("--min_unique_peptides", default="0")\n+ parser.add_option("--use_counterparts", default="false")\n+ parser.add_option("--min_ratio_count", default="2")\n+ parser.add_option("--lfq_min_ratio_count", default="2")\n+ parser.add_option("--calc_peak_properties", default="false")\n+ parser.add_option("--use_original_precursor_mz", default="false")\n+ parser.add_option("--multi_modification_search", default="false")\n+ parser.add_option("--lcms_run_type", default="0")\n+ parser.add_option("--reporter_type", default=None)\n+ parser.add_option("--output_mqpar", default=None)\n+ text_outputs = {\n+ "aif_msms": "aifMsms",\n+ "all_peptides": "allPeptides",\n+ "evidence": "evidence",\n+ "modification_specific_peptides": "modificationSpecificPeptides",\n+ "msms": "msms",\n+ "msms_scans": "msmsScans",\n+ "mz_range": "mzRange",\n+ "parameters": "parameters",\n+ "peptides": "peptides",\n+ "protein_groups": "proteinGroups",\n+ "sim_peptides": "simPeptides",\n+ "sim_scans": "simScans",\n+ "summary": "summary"\n+ }\n+ for output in text_outputs.keys():\n+ parser.add_option("--output_%s" % output, default=None)\n+\n+ parser.add_option("--variable_mods", default="Oxidation (M),Acetyl (Protein N-term)")\n+ parser.add_option("--restrict_mods", default="Oxidation (M),Acetyl (Protein N-term)")\n+ parser.add_option("--fixed_mods", default="Carbamidomethyl (C)")\n+\n+ add_fragment_options(parser)\n+\n+ (options, args) = parser.parse_args()\n+ options.restrict_mods = split_mods(options.restrict_mods)\n+ options.fixed_mods = split_mods(options.fixed_mods)\n+ options.variable_mods = split_mods(options.variable_mods)\n+\n+ update_fragment_settings(options)\n+\n+ raw_file_info = setup_inputs(options.input_groups)\n+ properties = get_properties(options)\n+ properties["raw_file_info"] = raw_file_info\n+ properties["isobaric_labels"] = build_isobaric_labels(options.reporter_type)\n+ set_group_params(properties, options)\n+ driver_contents = Template(TEMPLATE).substitute(properties)\n+ open("mqpar.xml", "w").write(driver_contents)\n+ print driver_contents\n+ execute("MaxQuantCmd.exe mqpar.xml %d" % options.num_cores)\n+ for key, basename in text_outputs.iteritems():\n+ attribute = "output_%s" % key\n+ destination = getattr(options, attribute, None)\n+ if destination:\n+ source = os.path.join("combined", "txt", "%s.txt" % basename)\n+ shutil.copy(source, destination)\n+ output_mqpar = options.output_mqpar\n+ if output_mqpar:\n+ shutil.copy("mqpar.xml", output_mqpar)\n+\n+if __name__ == \'__main__\':\n+ __main__()\n' |
| b |
| diff -r 000000000000 -r d4b6c9eae635 modifications.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/modifications.xml Fri May 10 17:22:51 2013 -0400 |
| b |
| b'@@ -0,0 +1,2580 @@\n+\xef\xbb\xbf<?xml version="1.0" encoding="utf-8"?>\r\n+<modifications xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">\r\n+ <modification index="0" title="Acetyl (K)" description="Acetylation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(2) H(2) O" create_date="2010-01-19T13:25:24.82357+01:00" last_modified_date="2010-01-19T14:15:40.2445414+01:00" user="neuhause" multi_modification="false">\r\n+ <position>notCterm</position>\r\n+ <modification_site index="0" site="K">\r\n+ <diagnostic_collection>\r\n+ <diagnostic name="acK*" shortname="acK*" composition="C(7) H(11) O N" />\r\n+ <diagnostic name="acK" shortname="acK" composition="C(7) H(14) O N(2)" />\r\n+ </diagnostic_collection>\r\n+ </modification_site>\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="1" title="Acetyl (Protein N-term)" description="Acetylation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(2) H(2) O" create_date="2010-01-19T14:27:34.5843488+01:00" last_modified_date="2010-01-19T14:28:09.7383488+01:00" user="neuhause" multi_modification="false">\r\n+ <position>proteinNterm</position>\r\n+ <modification_site index="0" site="-" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="2" title="Carbamidomethyl (C)" description="Iodoacetamide derivative" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(2) H(3) N O" create_date="2010-01-19T15:54:02.1976309+01:00" last_modified_date="2010-01-19T15:55:13.1353165+01:00" user="neuhause" multi_modification="false">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="C" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="3" title="Oxidation (M)" description="Oxidation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="O " create_date="2010-01-19T14:29:05.2191728+01:00" last_modified_date="2010-01-19T20:38:21.9609829+01:00" user="neuhause" multi_modification="false">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="M" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="4" title="Phospho (STY)" description="Phosphorylation" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="H O(3) P" create_date="2010-01-19T14:34:50.0721008+01:00" last_modified_date="2010-01-19T20:39:28.1471599+01:00" user="neuhause" multi_modification="false">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="S">\r\n+ <neutralloss_collection>\r\n+ <neutralloss name="H(3) O(4) P" shortname="H3 O4 P" composition="H(3) O(4) P" />\r\n+ </neutralloss_collection>\r\n+ </modification_site>\r\n+ <modification_site index="1" site="T">\r\n+ <neutralloss_collection>\r\n+ <neutralloss name="H(3) O(4) P" shortname="H3 O4 P" composition="H(3) O(4) P" />\r\n+ </neutralloss_collection>\r\n+ </modification_site>\r\n+ <modification_site index="2" site="Y">\r\n+ <diagnostic_collection>\r\n+ <diagnostic name="C(8) H(10) O(4) N P" shortname="pY" composition="C(8) H(10) O(4) N P" />\r\n+ </diagnostic_collection>\r\n+ </modification_site>\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="5" title="Arg6" description="Arginine-13C6 (R-13C6)" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="Cx(6) C(-6)" create_date="2010-01-19T14:37:21.2757206+01:00" last_modified_date="2010-01-23T19:17:45.328125+01:00" user="cox" multi_modification="false">\r\n+ <position>anywhere</position>\r\n+ <mod'..b'porterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="S H(3) C(2) N" create_date="2012-02-12T13:02:29.9546199+01:00" last_modified_date="2012-02-12T14:27:05.7229376+01:00" user="cox" multi_modification="true">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="S" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="463" title="Thr->CamCys" description="Thr->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="S H C N" create_date="2012-02-12T13:02:38.5970351+01:00" last_modified_date="2012-02-12T14:27:34.2241876+01:00" user="cox" multi_modification="true">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="T" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="464" title="Trp->CamCys" description="Trp->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="H(-2) C(-6) S O" create_date="2012-02-12T13:02:44.7434459+01:00" last_modified_date="2012-02-12T14:27:57.3434282+01:00" user="cox" multi_modification="true">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="W" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="465" title="Tyr->CamCys" description="Tyr->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-4) H(-1) S N" create_date="2012-02-12T13:02:53.7134616+01:00" last_modified_date="2012-02-12T14:28:23.6450744+01:00" user="cox" multi_modification="true">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="Y" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="466" title="Val->CamCys" description="Val->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="H(-1) S N O" create_date="2012-02-12T13:02:58.2686696+01:00" last_modified_date="2012-02-12T14:28:51.5067234+01:00" user="cox" multi_modification="true">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="V" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="467" title="Xle->CamCys" description="Leu/Ile->CamCys substitution" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-1) H(-3) S N O" create_date="2012-02-12T13:03:06.2714837+01:00" last_modified_date="2012-02-12T14:29:18.5727709+01:00" user="cox" multi_modification="true">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="I" />\r\n+ <modification_site index="1" site="L" />\r\n+ <type>standard</type>\r\n+ </modification>\r\n+ <modification index="468" title="Leu7" description="Leucine-13C6 15N1" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-6) Cx(6) N(-1) Nx" create_date="2012-03-14T11:27:13.8771423+01:00" last_modified_date="2012-03-14T11:30:52.8703269+01:00" user="cox" multi_modification="false">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="L" />\r\n+ <type>label</type>\r\n+ </modification>\r\n+ <modification index="469" title="Ile7" description="Isoleucine-13C6 15N1" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" composition="C(-6) Cx(6) N(-1) Nx" create_date="2012-06-11T21:21:24.4946343+02:00" last_modified_date="2012-06-11T21:21:24.4946343+02:00" user="cox" multi_modification="false">\r\n+ <position>anywhere</position>\r\n+ <modification_site index="0" site="I" />\r\n+ <type>label</type>\r\n+ </modification>\r\n+</modifications>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r d4b6c9eae635 proteases.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteases.xml Fri May 10 17:22:51 2013 -0400 |
| b |
| @@ -0,0 +1,1 @@ +<?xml version="1.0" encoding="utf-8"?><proteases xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><protease name="Trypsin" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="P" /></protease><protease name="Arg-C" semispecific="false"><rule index="1" sense="C-Term" cleave="R" restrict="P" /></protease><protease name="Asp-N" semispecific="false"><rule index="1" sense="N-Term" cleave="D" restrict="" /></protease><protease name="Asp-N_ambic" semispecific="false"><rule index="1" sense="N-Term" cleave="DE" restrict="" /></protease><protease name="Chymotrypsin" semispecific="false"><rule index="1" sense="C-Term" cleave="FLWY" restrict="P" /></protease><protease name="CNBr" semispecific="false"><rule index="1" sense="C-Term" cleave="M" restrict="" /></protease><protease name="CNBr+Trypsin" semispecific="false"><rule index="1" sense="C-Term" cleave="M" restrict="" /><rule index="2" sense="C-Term" cleave="KR" restrict="P" /></protease><protease name="Formic_acid" semispecific="false"><rule index="1" sense="C-Term" cleave="D" restrict="" /></protease><protease name="Lys-C" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="P" /></protease><protease name="Lys-C/P" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="" /></protease><protease name="PepsinA" semispecific="false"><rule index="1" sense="C-Term" cleave="FL" restrict="" /></protease><protease name="Tryp-CNBr" semispecific="false"><rule index="1" sense="C-Term" cleave="KMR" restrict="P" /></protease><protease name="TrypChymo" semispecific="false"><rule index="1" sense="C-Term" cleave="FKLRWY" restrict="P" /></protease><protease name="Trypsin/P" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="" /></protease><protease name="Trypsin/P+DP" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="ACDEFGHIJKLMNQRSTVWY" /></protease><protease name="V8-DE" semispecific="false"><rule index="1" sense="C-Term" cleave="DE" restrict="P" /></protease><protease name="V8-E" semispecific="false"><rule index="1" sense="C-Term" cleave="E" restrict="P" /></protease><protease name="semiTrypsin" semispecific="true"><rule index="1" sense="C-Term" cleave="KR" restrict="P" /></protease><protease name="LysC+AspN" semispecific="false"><rule index="1" sense="N-Term" cleave="D" restrict="" /><rule index="2" sense="C-Term" cleave="K" restrict="P" /></protease><protease name="Lys-C/P+DP" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="ACDEFGHIJKLMNQRSTVWY" /></protease><protease name="Trypsin/P + Asp-N" semispecific="false"><rule index="1" sense="N-Term" cleave="D" restrict="" /><rule index="2" sense="C-Term" cleave="KR" restrict="" /></protease><protease name="Asp-C" semispecific="false"><rule index="1" sense="C-Term" cleave="D" restrict="" /></protease><protease name="Trypsin/P+Asp-C" semispecific="false"><rule index="1" sense="C-Term" cleave="KR" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="" /></protease><protease name="SemiLys" semispecific="true"><rule index="1" sense="C-Term" cleave="K" restrict="" /></protease><protease name="SemiGluC" semispecific="true"><rule index="1" sense="C-Term" cleave="DE" restrict="" /></protease><protease name="LysC/P+AspC" semispecific="false"><rule index="1" sense="C-Term" cleave="K" restrict="" /><rule index="2" sense="C-Term" cleave="D" restrict="" /></protease><protease name="GluC" semispecific="false"><rule index="1" sense="C-Term" cleave="E" restrict="" /></protease></proteases> \ No newline at end of file |
| b |
| diff -r 000000000000 -r d4b6c9eae635 unimod.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/unimod.xml Fri May 10 17:22:51 2013 -0400 |
| b |
| b'@@ -0,0 +1,15140 @@\n+\xef\xbb\xbf<?xml version="1.0" encoding="utf-8"?>\n+<!--Copyright (C) 2002-2006 Unimod; this information may be copied, distributed and/or-->\n+<!--modified under certain conditions, but it comes WITHOUT ANY WARRANTY; see the-->\n+<!--accompanying Design Science License for more details-->\n+<umod:unimod xmlns:umod="http://www.unimod.org/xmlns/schema/unimod_2"\n+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\n+ xsi:schemaLocation="http://www.unimod.org/xmlns/schema/unimod_2 http://www.unimod.org/xmlns/schema/unimod_2/unimod_2.xsd"\n+ majorVersion="2"\n+ minorVersion="0">\n+ <umod:elements>\n+ <umod:elem title="H" full_name="Hydrogen" avge_mass="1.00794" mono_mass="1.007825035"/>\n+ <umod:elem title="2H" full_name="Deuterium" avge_mass="2.014101779"\n+ mono_mass="2.014101779"/>\n+ <umod:elem title="Li" full_name="Lithium" avge_mass="6.941" mono_mass="7.016003"/>\n+ <umod:elem title="C" full_name="Carbon" avge_mass="12.0107" mono_mass="12"/>\n+ <umod:elem title="13C" full_name="Carbon13" avge_mass="13.00335483"\n+ mono_mass="13.00335483"/>\n+ <umod:elem title="N" full_name="Nitrogen" avge_mass="14.0067" mono_mass="14.003074"/>\n+ <umod:elem title="15N" full_name="Nitrogen15" avge_mass="15.00010897"\n+ mono_mass="15.00010897"/>\n+ <umod:elem title="O" full_name="Oxygen" avge_mass="15.9994" mono_mass="15.99491463"/>\n+ <umod:elem title="18O" full_name="Oxygen18" avge_mass="17.9991603" mono_mass="17.9991603"/>\n+ <umod:elem title="F" full_name="Fluorine" avge_mass="18.9984032" mono_mass="18.99840322"/>\n+ <umod:elem title="Na" full_name="Sodium" avge_mass="22.98977" mono_mass="22.9897677"/>\n+ <umod:elem title="P" full_name="Phosphorous" avge_mass="30.973761" mono_mass="30.973762"/>\n+ <umod:elem title="S" full_name="Sulfur" avge_mass="32.065" mono_mass="31.9720707"/>\n+ <umod:elem title="Cl" full_name="Chlorine" avge_mass="35.453" mono_mass="34.96885272"/>\n+ <umod:elem title="K" full_name="Potassium" avge_mass="39.0983" mono_mass="38.9637074"/>\n+ <umod:elem title="Ca" full_name="Calcium" avge_mass="40.078" mono_mass="39.9625906"/>\n+ <umod:elem title="Fe" full_name="Iron" avge_mass="55.845" mono_mass="55.9349393"/>\n+ <umod:elem title="Ni" full_name="Nickel" avge_mass="58.6934" mono_mass="57.9353462"/>\n+ <umod:elem title="Zn" full_name="Zinc" avge_mass="65.409" mono_mass="63.9291448"/>\n+ <umod:elem title="Se" full_name="Selenium" avge_mass="78.96" mono_mass="79.9165196"/>\n+ <umod:elem title="Br" full_name="Bromine" avge_mass="79.904" mono_mass="78.9183361"/>\n+ <umod:elem title="Ag" full_name="Silver" avge_mass="107.8682" mono_mass="106.905092"/>\n+ <umod:elem title="Hg" full_name="Mercury" avge_mass="200.59" mono_mass="201.970617"/>\n+ <umod:elem title="Au" full_name="Gold" avge_mass="196.96655" mono_mass="196.966543"/>\n+ <umod:elem title="I" full_name="Iodine" avge_mass="126.90447" mono_mass="126.904473"/>\n+ <umod:elem title="Mo" full_name="Molybdenum" avge_mass="95.94" mono_mass="97.9054073"/>\n+ <umod:elem title="Cu" full_name="Copper" avge_mass="63.546" mono_mass="62.9295989"/>\n+ <umod:elem title="e" full_name="electron" avge_mass="0.000549" mono_mass="0.000549"/>\n+ <umod:elem title="B" full_name="Boron" avge_mass="10.811" mono_mass="11.0093055"/>\n+ <umod:elem title="As" full_name="Arsenic" avge_mass="74.9215942" mono_mass="74.9215942"/>\n+ </umod:elements>\n+ <umod:modifications>\n+ <umod:mod title="Acetyl" full_name="Acetylation" username_of_poster="unimod"\n+ group_of_poster="admin"\n+ date_time_posted="2002-08-19 19:17:11"\n+ date_time_modified="2008-02-15 05:20:02"\n+ approved="1"\n+ record_id="1">\n+ <umod:specificity hidden="1" site="T" position="Anywhere" classification="Post-translational"\n+ '..b'element symbol="H" number="1"/>\n+ <umod:element symbol="P" number="1"/>\n+ <umod:element symbol="O" number="3"/>\n+ </umod:brick>\n+ <umod:brick title="Sulf" full_name="Sulfate" mono_mass="79.95681459000001"\n+ avge_mass="80.0632">\n+ <umod:element symbol="S" number="1"/>\n+ <umod:element symbol="O" number="3"/>\n+ </umod:brick>\n+ <umod:brick title="Pent" full_name="Pentose" mono_mass="132.0422588" avge_mass="132.11462">\n+ <umod:element symbol="C" number="5"/>\n+ <umod:element symbol="H" number="8"/>\n+ <umod:element symbol="O" number="4"/>\n+ </umod:brick>\n+ <umod:brick title="Li" full_name="Lithium" mono_mass="7.016003" avge_mass="6.941">\n+ <umod:element symbol="Li" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="13C" full_name="Carbon 13" mono_mass="13.00335483"\n+ avge_mass="13.00335483">\n+ <umod:element symbol="13C" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="15N" full_name="Nitrogen 15" mono_mass="15.00010897"\n+ avge_mass="15.00010897">\n+ <umod:element symbol="15N" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Cl" full_name="Chlorine" mono_mass="34.96885272" avge_mass="35.453">\n+ <umod:element symbol="Cl" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="K" full_name="Potassium" mono_mass="38.9637074" avge_mass="39.0983">\n+ <umod:element symbol="K" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Ca" full_name="Calcium" mono_mass="39.9625906" avge_mass="40.078">\n+ <umod:element symbol="Ca" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Fe" full_name="Iron" mono_mass="55.9349393" avge_mass="55.845">\n+ <umod:element symbol="Fe" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Ni" full_name="Nickel" mono_mass="57.9353462" avge_mass="58.6934">\n+ <umod:element symbol="Ni" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Zn" full_name="Zinc" mono_mass="63.9291448" avge_mass="65.409">\n+ <umod:element symbol="Zn" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Br" full_name="Bromine" mono_mass="78.9183361" avge_mass="79.904">\n+ <umod:element symbol="Br" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Ag" full_name="Silver" mono_mass="106.905092" avge_mass="107.8682">\n+ <umod:element symbol="Ag" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Hg" full_name="Mercury" mono_mass="201.970617" avge_mass="200.59">\n+ <umod:element symbol="Hg" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Au" full_name="Gold" mono_mass="196.966543" avge_mass="196.96655">\n+ <umod:element symbol="Au" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="I" full_name="Iodine" mono_mass="126.904473" avge_mass="126.90447">\n+ <umod:element symbol="I" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Mo" full_name="Molybdenum" mono_mass="97.9054073" avge_mass="95.94">\n+ <umod:element symbol="Mo" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Cu" full_name="Copper" mono_mass="62.9295989" avge_mass="63.546">\n+ <umod:element symbol="Cu" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="Hep" full_name="Heptose" mono_mass="192.06338820000002"\n+ avge_mass="192.16658">\n+ <umod:element symbol="C" number="7"/>\n+ <umod:element symbol="H" number="12"/>\n+ <umod:element symbol="O" number="6"/>\n+ </umod:brick>\n+ <umod:brick title="B" full_name="Boron" mono_mass="11.0093055" avge_mass="10.811">\n+ <umod:element symbol="B" number="1"/>\n+ </umod:brick>\n+ <umod:brick title="As" full_name="Arsenic" mono_mass="74.9215942" avge_mass="74.9215942">\n+ <umod:element symbol="As" number="1"/>\n+ </umod:brick>\n+ </umod:mod_bricks>\n+</umod:unimod>\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r d4b6c9eae635 update.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Fri May 10 17:22:51 2013 -0400 |
| [ |
| @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$LICENSE_FILE" ]; +then + wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" +fi + +# Run repository specific update actions. +if [ -f update_repo.sh ]; +then + ./update_repo.sh +fi + +wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md + +# Create repository README +if [ ! -e README_REPO.md ]; +then + echo "TODO: Document this tool repository." > README_REPO.md +fi +cat README_REPO.md README_GALAXYP.md > README.md + + +# If version file exists, update all tools to this version +VERSION_FILE=version +if [ -e "$VERSION_FILE" ]; +then + VERSION=`cat $VERSION_FILE` + + # Replace tool version in each tool XML file ` + find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; + +fi |