# HG changeset patch
# User galaxyp
# Date 1368223102 14400
# Node ID 0578e296cab45cff7d55e2f3efbf144a82ac0579
Initial commit.
diff -r 000000000000 -r 0578e296cab4 LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Fri May 10 17:58:22 2013 -0400
@@ -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]
+
diff -r 000000000000 -r 0578e296cab4 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,40 @@
+Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
+of mgf files and performs X! Tandem and OMSSA searches on these via
+SearchGUI and merges the results using PeptideShaker.
+
+For Galaxy-P we are installing this tool via CloudBioLinux
+(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
+this fabric script may not be exactly appropriate for your environment
+it may serve as a template for how to install this software. In
+particular these tools require CLI wrappers to be placed for
+PeptideShaker and SearchGUI that can be installed as demostrated in
+these fabric functions.
+
+Note: Also SearchGUI requires a version greater than 1.12.2 which
+contained several bugs preventing this from working on the
+command-line and via Linux.
+
+Also, PeptideShaker may require xvfb to simulate an X environment if
+this is installed on a headless server.
+# 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.
diff -r 000000000000 -r 0578e296cab4 README_GALAXYP.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md Fri May 10 17:58:22 2013 -0400
@@ -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.
diff -r 000000000000 -r 0578e296cab4 README_REPO.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,18 @@
+Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
+of mgf files and performs X! Tandem and OMSSA searches on these via
+SearchGUI and merges the results using PeptideShaker.
+
+For Galaxy-P we are installing this tool via CloudBioLinux
+(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
+this fabric script may not be exactly appropriate for your environment
+it may serve as a template for how to install this software. In
+particular these tools require CLI wrappers to be placed for
+PeptideShaker and SearchGUI that can be installed as demostrated in
+these fabric functions.
+
+Note: Also SearchGUI requires a version greater than 1.12.2 which
+contained several bugs preventing this from working on the
+command-line and via Linux.
+
+Also, PeptideShaker may require xvfb to simulate an X environment if
+this is installed on a headless server.
diff -r 000000000000 -r 0578e296cab4 build_mods_loc.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/build_mods_loc.py Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+
+import xml.etree.ElementTree as ET
+from os.path import exists
+
+with open("searchgui_mods.loc", "w") as output:
+ for mods_path in ["searchGUI_mods.xml", "searchGUI_usermods.xml"]:
+ tree = ET.parse(mods_path)
+ modifications_el = tree.getroot()
+ for mod in modifications_el.findall("{http://www.ncbi.nlm.nih.gov}MSModSpec"):
+ name_el = mod.find("{http://www.ncbi.nlm.nih.gov}MSModSpec_name")
+ output.write("%s\n" % name_el.text.lower())
diff -r 000000000000 -r 0578e296cab4 peptide_shaker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peptide_shaker.xml Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,221 @@
+
+
+
+ Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
+
+
+ mkdir spectra;
+ mkdir output;
+ mkdir output_reports;
+ cwd=`pwd`;
+ #for $mgf in $peak_lists:
+ #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
+ ln -s '$mgf' 'spectra/$input_name';
+ #end for
+ SearchCLI \
+ -spectrum_files \$cwd/spectra \
+ -output_folder \$cwd/output \
+ -ppm $precursor_ion_tol_units \
+ -prec_tol $precursor_ion_tol \
+ -frag_tol $fragment_tol \
+ -enzyme '$enzyme' \
+ #set $fixed_mods_str = $fixed_modifications or ''
+ #set $variable_mods_str = $variable_modifications or ''
+ #if $fixed_mods_str
+ -fixed_mods "$fixed_mods_str" \
+ #end if
+ #if $variable_mods_str
+ -variable_mods "$variable_mods_str" \
+ #end if
+ -mc $missed_cleavages \
+ #if $advanced.specify:
+ -xtandem $advanced.xtandem \
+ #if $advanced.omssa.run_omssa
+ #set $omssa = 1
+ #else
+ #set $omssa = 0
+ #end if
+ -omssa $omssa \
+ #if $omssa == 1
+ -hitlist_length ${advanced.omssa.hitlist_length} \
+ -remove_prec ${advanced.omssa.remove_precursor} \
+ -scale_prec ${advanced.omssa.scale_precursor} \
+ -estimate_charge ${advanced.omssa.estimate_charge} \
+ #end if
+ #end if
+ -db $input_database;
+ PeptideShakerCLI \
+ -experiment 'Galaxy Experiment' \
+ -sample 'Sample' \
+ -replicate 1 \
+ -spectrum_files \$cwd/spectra \
+ -identification_files \$cwd/output \
+ -search_params \$cwd/output/SearchGUI.parameters \
+ -out_txt_1 \$cwd/output_reports \
+ #if $processing_options.specify
+ -protein_FDR ${processing_options.protein_fdr} \
+ -peptide_FDR ${processing_options.peptide_fdr} \
+ -psm_FDR ${processing_options.psm_fdr} \
+ -psm_FLR ${processing_options.psm_flr} \
+ #if str($processing_options.a_score.use) == "1"
+ #set $a_score = 1
+ #else
+ #set $a_score = 0
+ #end if
+ -a_score $a_score \
+ #if str($a_score) == "1"
+ -a_score_neutral_losses ${processing_options.a_score.neutral_losses} \
+ #end if
+ #end if
+ #if $filtering_options.specify
+ -min_peptide_length ${filtering_options.min_peptide_length} \
+ -max_peptide_length ${filtering_options.max_peptide_length} \
+ -max_precursor_error ${filtering_options.max_precursor_error} \
+ -max_precursor_error_type ${filtering_options.max_precursor_error_type} \
+ -max_xtandem_e ${filtering_options.max_xtandem_e} \
+ -max_omssa_e ${filtering_options.max_omssa_e} \
+ -exclude_unknown_ptms ${filtering_options.exclude_unknown_ptms} \
+ #end if
+ -out \$cwd/output.cps ;
+ mv output_reports/*peptides.txt peptides.txt ;
+ mv output_reports/*psms.txt psms.txt ;
+ mv output_reports/*proteins.txt proteins.txt
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ peptide_shaker
+ searchgui
+
+
+**What it does**
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `TODO`
+
+If you use this tool in Galaxy, please cite TODO
+
+
diff -r 000000000000 -r 0578e296cab4 searchGUI_mods.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/searchGUI_mods.xml Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,3021 @@
+
+
+
+
+ 0
+
+
+ 0
+
+ methylation of K
+ 14.015650
+ 14.0266
+ 0
+
+ K
+
+ 34
+ Methyl
+
+
+
+ 1
+
+
+ 0
+
+ oxidation of M
+ 15.994915
+ 15.9994
+ 0
+
+ M
+
+ 35
+ Oxidation
+
+
+
+ 2
+
+
+ 0
+
+ carboxymethyl C
+ 58.005479
+ 58.0361
+ 0
+
+ C
+
+ 6
+ Carboxymethyl
+
+
+
+ 3
+
+
+ 0
+
+ carbamidomethyl C
+ 57.021464
+ 57.0513
+ 0
+
+ C
+
+ 4
+ Carbamidomethyl
+
+
+
+ 4
+
+
+ 0
+
+ deamidation of N and Q
+ 0.984016
+ 0.9848
+ 0
+
+ N
+ Q
+
+ 7
+ Deamidated
+
+
+
+ 5
+
+
+ 0
+
+ propionamide C
+ 71.037114
+ 71.0779
+ 0
+
+ C
+
+ 24
+ Propionamide
+
+
+
+ 6
+
+
+ 0
+
+ phosphorylation of S
+ 79.966331
+ 79.9799
+ 0
+
+ S
+
+ 21
+ Phospho
+
+
+
+ 7
+
+
+ 0
+
+ phosphorylation of T
+ 79.966331
+ 79.9799
+ 0
+
+ T
+
+ 21
+ Phospho
+
+
+
+ 8
+
+
+ 0
+
+ phosphorylation of Y
+ 79.966331
+ 79.9799
+ 0
+
+ Y
+
+ 21
+ Phospho
+
+
+
+ 9
+
+
+ 2
+
+ M cleavage from protein n-term
+ -131.040485
+ -131.1961
+ 0
+
+ M
+
+ 765
+ Met-loss
+
+
+
+ 10
+
+
+ 1
+
+ acetylation of protein n-term
+ 42.010565
+ 42.0367
+ 0
+ 1
+ Acetyl
+
+
+
+ 11
+
+
+ 1
+
+ methylation of protein n-term
+ 14.015650
+ 14.0266
+ 0
+ 34
+ Methyl
+
+
+
+ 12
+
+
+ 1
+
+ tri-methylation of protein n-term
+ 42.046950
+ 42.0797
+ 0
+ 37
+ Trimethyl
+
+
+
+ 13
+
+
+ 0
+
+ beta methythiolation of D
+ 45.987721
+ 46.0916
+ 0
+
+ D
+
+ 39
+ Methylthio
+
+
+
+ 14
+
+
+ 0
+
+ methylation of Q
+ 14.015650
+ 14.0266
+ 0
+
+ Q
+
+ 34
+ Methyl
+
+
+
+ 15
+
+
+ 0
+
+ tri-methylation of K
+ 42.046950
+ 42.0797
+ 0
+
+ K
+
+ 37
+ Trimethyl
+
+
+
+ 16
+
+
+ 0
+
+ methylation of D
+ 14.015650
+ 14.0266
+ 0
+
+ D
+
+ 34
+ Methyl
+
+
+
+ 17
+
+
+ 0
+
+ methylation of E
+ 14.015650
+ 14.0266
+ 0
+
+ E
+
+ 34
+ Methyl
+
+
+
+ 18
+
+
+ 7
+
+ methylation of peptide c-term
+ 14.015650
+ 14.0266
+ 0
+ 34
+ Methyl
+
+
+
+ 19
+
+
+ 0
+
+ tri-deuteromethylation of D
+ 17.034480
+ 17.0451
+ 0
+
+ D
+
+ 298
+ Methyl:2H(3)
+
+
+
+ 20
+
+
+ 0
+
+ tri-deuteromethylation of E
+ 17.034480
+ 17.0451
+ 0
+
+ E
+
+ 298
+ Methyl:2H(3)
+
+
+
+ 21
+
+
+ 7
+
+ tri-deuteromethylation of peptide c-term
+ 17.034480
+ 17.0451
+ 0
+ 298
+ Methyl:2H(3)
+
+
+
+ 22
+
+
+ 1
+
+ n-formyl met addition
+ 159.035399
+ 159.2062
+ 0
+ 107
+ FormylMet
+
+
+
+ 23
+
+
+ 0
+
+ 2-amino-3-oxo-butanoic acid T
+ -2.015650
+ -2.0159
+ 0
+
+ T
+
+ 401
+ Didehydro
+
+
+
+ 24
+
+
+ 0
+
+ acetylation of K
+ 42.010565
+ 42.0367
+ 0
+
+ K
+
+ 1
+ Acetyl
+
+
+
+ 25
+
+
+ 7
+
+ amidation of peptide c-term
+ -0.984016
+ -0.9848
+ 0
+ 2
+ Amidated
+
+
+
+ 26
+
+
+ 0
+
+ beta-methylthiolation of D (duplicate of 13)
+ 45.987721
+ 46.0916
+ 0
+
+ D
+
+ 39
+ Methylthio
+
+
+
+ 27
+
+
+ 0
+
+ carboxyamidomethylation of K
+ 57.021464
+ 57.0513
+ 0
+
+ K
+
+ 4
+ Carbamidomethyl
+
+
+
+ 28
+
+
+ 0
+
+ carboxyamidomethylation of H
+ 57.021464
+ 57.0513
+ 0
+
+ H
+
+ 4
+ Carbamidomethyl
+
+
+
+ 29
+
+
+ 0
+
+ carboxyamidomethylation of D
+ 57.021464
+ 57.0513
+ 0
+
+ D
+
+ 4
+ Carbamidomethyl
+
+
+
+ 30
+
+
+ 0
+
+ carboxyamidomethylation of E
+ 57.021464
+ 57.0513
+ 0
+
+ E
+
+ 4
+ Carbamidomethyl
+
+
+
+ 31
+
+
+ 0
+
+ carbamylation of K
+ 43.005814
+ 43.0247
+ 0
+
+ K
+
+ 5
+ Carbamyl
+
+
+
+ 32
+
+
+ 5
+
+ carbamylation of n-term peptide
+ 43.005814
+ 43.0247
+ 0
+
+ X
+
+ 5
+ Carbamyl
+
+
+
+ 33
+
+
+ 0
+
+ citrullination of R
+ 0.984016
+ 0.9848
+ 0
+
+ R
+
+ 7
+ Deamidated
+
+
+
+ 34
+
+
+ 0
+
+ oxidation of C to cysteic acid
+ 47.984744
+ 47.9982
+ 0
+
+ C
+
+ 345
+ Trioxidation
+
+
+
+ 35
+
+
+ 0
+
+ di-iodination of Y
+ 251.793296
+ 251.7931
+ 0
+
+ Y
+
+ 130
+ Diiodo
+
+
+
+ 36
+
+
+ 0
+
+ di-methylation of K
+ 28.031300
+ 28.0532
+ 0
+
+ K
+
+ 36
+ Dimethyl
+
+
+
+ 37
+
+
+ 0
+
+ di-methylation of R
+ 28.031300
+ 28.0532
+ 0
+
+ R
+
+ 36
+ Dimethyl
+
+
+
+ 38
+
+
+ 5
+
+ di-methylation of peptide n-term
+ 28.031300
+ 28.0532
+ 0
+ 36
+ Dimethyl
+
+
+
+ 39
+
+
+ 0
+
+ oxidation of F to dihydroxyphenylalanine
+ 31.989829
+ 31.9988
+ 0
+
+ F
+
+ 425
+ Dioxidation
+
+
+
+ 40
+
+
+ 0
+
+ gammathiopropionylation of K
+ 87.998285
+ 88.1283
+ 0
+
+ K
+
+ 126
+ Thioacyl
+
+
+
+ 41
+
+
+ 5
+
+ gammathiopropionylation of peptide n-term
+ 87.998285
+ 88.1283
+ 0
+ 126
+ Thioacyl
+
+
+
+ 42
+
+
+ 0
+
+ farnesylation of C
+ 204.187801
+ 204.3511
+ 0
+
+ C
+
+ 44
+ Farnesyl
+
+
+
+ 43
+
+
+ 0
+
+ formylation of K
+ 27.994915
+ 28.0101
+ 0
+
+ K
+
+ 122
+ Formyl
+
+
+
+ 44
+
+
+ 5
+
+ formylation of peptide n-term
+ 27.994915
+ 28.0101
+ 0
+ 122
+ Formyl
+
+
+
+ 45
+
+
+ 0
+
+ oxidation of W to formylkynurenin
+ 31.989829
+ 31.9988
+ 0
+
+ W
+
+ 425
+ Dioxidation
+
+
+
+ 46
+
+
+ 0
+
+ fluorophenylalanine
+ 17.990578
+ 17.9905
+ 0
+
+ F
+
+ 127
+ Fluoro
+
+
+
+ 47
+
+
+ 0
+
+ beta-carboxylation of D
+ 43.989829
+ 44.0095
+ 0
+
+ D
+
+ 299
+ Carboxy
+
+
+
+ 48
+
+
+ 0
+
+ gamma-carboxylation of E
+ 43.989829
+ 44.0095
+ 0
+
+ E
+
+ 299
+ Carboxy
+
+
+
+ 49
+
+
+ 0
+
+ geranyl-geranyl
+ 272.250401
+ 272.4681
+ 0
+
+ C
+
+ 48
+ GeranylGeranyl
+
+
+
+ 50
+
+
+ 2
+
+ glucuronylation of protein n-term
+ 176.032088
+ 176.1241
+ 0
+
+ G
+
+ 54
+ Glucuronyl
+
+
+
+ 51
+
+
+ 0
+
+ glutathione disulfide
+ 305.068156
+ 305.3076
+ 0
+
+ C
+
+ 55
+ Glutathione
+
+
+
+ 52
+
+
+ 0
+
+ ubiquitinylation residue
+ 114.042927
+ 114.1026
+ 0
+
+ K
+
+ 121
+ GlyGly
+
+
+
+ 53
+
+
+ 0
+
+ guanidination of K
+ 42.021798
+ 42.0400
+ 0
+
+ K
+
+ 52
+ Guanidinyl
+
+
+
+ 54
+
+
+ 0
+
+ oxidation of H to N
+ -23.015984
+ -23.0366
+ 0
+
+ H
+
+ 348
+ His->Asn
+
+
+
+ 55
+
+
+ 0
+
+ oxidation of H to D
+ -22.031969
+ -22.0519
+ 0
+
+ D
+
+ 349
+ His->Asp
+
+
+
+ 56
+
+
+ 8
+
+ homoserine
+ -29.992806
+ -30.0922
+ 0
+
+ M
+
+ 10
+ Met->Hse
+
+
+
+ 57
+
+
+ 8
+
+ homoserine lactone
+ -48.003371
+ -48.1075
+ 0
+
+ M
+
+ 11
+ Met->Hsl
+
+
+
+ 58
+
+
+ 0
+
+ oxidation of W to hydroxykynurenin
+ 19.989829
+ 19.9881
+ 0
+
+ W
+
+ 350
+ Trp->Hydroxykynurenin
+
+
+
+ 59
+
+
+ 0
+
+ hydroxylation of D
+ 15.994915
+ 15.9994
+ 0
+
+ D
+
+ 35
+ Oxidation
+
+
+
+ 60
+
+
+ 0
+
+ hydroxylation of K
+ 15.994915
+ 15.9994
+ 0
+
+ K
+
+ 35
+ Oxidation
+
+
+
+ 61
+
+
+ 0
+
+ hydroxylation of N
+ 15.994915
+ 15.9994
+ 0
+
+ N
+
+ 35
+ Oxidation
+
+
+
+ 62
+
+
+ 0
+
+ hydroxylation of P
+ 15.994915
+ 15.9994
+ 0
+
+ P
+
+ 35
+ Oxidation
+
+
+
+ 63
+
+
+ 0
+
+ hydroxylation of F
+ 15.994915
+ 15.9994
+ 0
+
+ F
+
+ 35
+ Oxidation
+
+
+
+ 64
+
+
+ 0
+
+ hydroxylation of Y
+ 15.994915
+ 15.9994
+ 0
+
+ Y
+
+ 35
+ Oxidation
+
+
+
+ 65
+
+
+ 0
+
+ iodination of Y
+ 125.896648
+ 125.8965
+ 0
+
+ Y
+
+ 129
+ Iodo
+
+
+
+ 66
+
+
+ 0
+
+ oxidation of W to kynurenin
+ 3.994915
+ 3.9887
+ 0
+
+ W
+
+ 351
+ Trp->Kynurenin
+
+
+
+ 67
+
+
+ 0
+
+ lipoyl K
+ 188.032956
+ 188.3103
+ 0
+
+ K
+
+ 42
+ Lipoyl
+
+
+
+ 68
+
+
+ 7
+
+ methyl ester of peptide c-term (duplicate of 18)
+ 14.015650
+ 14.0266
+ 0
+ 34
+ Methyl
+
+
+
+ 69
+
+
+ 0
+
+ methyl ester of D
+ 14.015650
+ 14.0266
+ 0
+
+ D
+
+ 34
+ Methyl
+
+
+
+ 70
+
+
+ 0
+
+ methyl ester of E (duplicate of 17)
+ 14.015650
+ 14.0266
+ 0
+
+ E
+
+ 34
+ Methyl
+
+
+
+ 71
+
+
+ 0
+
+ methyl ester of S
+ 14.015650
+ 14.0266
+ 0
+
+ S
+
+ 34
+ Methyl
+
+
+
+ 72
+
+
+ 0
+
+ methyl ester of Y
+ 14.015650
+ 14.0266
+ 0
+
+ Y
+
+ 34
+ Methyl
+
+
+
+ 73
+
+
+ 0
+
+ methyl C
+ 14.015650
+ 14.0266
+ 0
+
+ C
+
+ 34
+ Methyl
+
+
+
+ 74
+
+
+ 0
+
+ methyl H
+ 14.015650
+ 14.0266
+ 0
+
+ H
+
+ 34
+ Methyl
+
+
+
+ 75
+
+
+ 0
+
+ methyl N
+ 14.015650
+ 14.0266
+ 0
+
+ N
+
+ 34
+ Methyl
+
+
+
+ 76
+
+
+ 5
+
+ methylation of peptide n-term
+ 14.015650
+ 14.0266
+ 0
+ 34
+ Methyl
+
+
+
+ 77
+
+
+ 0
+
+ methyl R
+ 14.015650
+ 14.0266
+ 0
+
+ R
+
+ 34
+ Methyl
+
+
+
+ 78
+
+
+ 2
+
+ myristoleylation of G
+ 208.182715
+ 208.3398
+ 0
+
+ G
+
+ 134
+ Myristoleyl
+
+
+
+ 79
+
+
+ 2
+
+ myristoyl-4H of G
+ 206.167065
+ 206.3239
+ 0
+
+ G
+
+ 135
+ Myristoyl+Delta:H(-4)
+
+
+
+ 80
+
+
+ 6
+
+ myristoylation of peptide n-term G
+ 210.198366
+ 210.3556
+ 0
+
+ G
+
+ 45
+ Myristoyl
+
+
+
+ 81
+
+
+ 0
+
+ myristoylation of K
+ 210.198366
+ 210.3556
+ 0
+
+ K
+
+ 45
+ Myristoyl
+
+
+
+ 82
+
+
+ 1
+
+ formylation of protein n-term
+ 27.994915
+ 28.0101
+ 0
+ 122
+ Formyl
+
+
+
+ 83
+
+
+ 0
+
+ NEM C
+ 125.047679
+ 125.1253
+ 0
+
+ C
+
+ 108
+ Nethylmaleimide
+
+
+
+ 84
+
+
+ 0
+
+ NIPCAM
+ 99.068414
+ 99.1311
+ 0
+
+ C
+
+ 17
+ NIPCAM
+
+
+
+ 85
+
+
+ 0
+
+ oxidation of W to nitro
+ 44.985078
+ 44.9976
+ 0
+
+ W
+
+ 354
+ Nitro
+
+
+
+ 86
+
+
+ 0
+
+ oxidation of Y to nitro
+ 44.985078
+ 44.9976
+ 0
+
+ Y
+
+ 354
+ Nitro
+
+
+
+ 87
+
+
+ 5
+
+ O18 on peptide n-term
+ 2.004246
+ 1.9998
+ 0
+ 258
+ Label:18O(1)
+
+
+
+ 88
+
+
+ 5
+
+ di-O18 on peptide n-term
+ 4.00849
+ 3.9995
+ 0
+ 193
+ Label:18O(2)
+
+
+
+ 89
+
+
+ 0
+
+ oxidation of H
+ 15.994915
+ 15.9994
+ 0
+
+ H
+
+ 35
+ Oxidation
+
+
+
+ 90
+
+
+ 0
+
+ oxidation of W
+ 15.994915
+ 15.9994
+ 0
+
+ W
+
+ 35
+ Oxidation
+
+
+
+ 91
+
+
+ 0
+
+ phosphopantetheine S
+ 340.085794
+ 340.3330
+ 0
+
+ S
+
+ 49
+ Phosphopantetheine
+
+
+
+ 92
+
+
+ 0
+
+ palmitoylation of C
+ 238.229666
+ 238.4088
+ 0
+
+ C
+
+ 47
+ Palmitoyl
+
+
+
+ 93
+
+
+ 0
+
+ palmitoylation of K
+ 238.229666
+ 238.4088
+ 0
+
+ K
+
+ 47
+ Palmitoyl
+
+
+
+ 94
+
+
+ 0
+
+ palmitoylation of S
+ 238.229666
+ 238.4088
+ 0
+
+ S
+
+ 47
+ Palmitoyl
+
+
+
+ 95
+
+
+ 0
+
+ palmitoylation of T
+ 238.229666
+ 238.4088
+ 0
+
+ T
+
+ 47
+ Palmitoyl
+
+
+
+ 96
+
+
+ 0
+
+ phosphorylation of S with prompt loss
+ -18.010565
+ -18.0153
+ 0
+
+ S
+
+ 23
+ Dehydrated
+
+
+
+ 97
+
+
+ 0
+
+ phosphorylation of T with prompt loss
+ -18.010565
+ -18.0153
+ 0
+
+ T
+
+ 23
+ Dehydrated
+
+
+
+ 98
+
+
+ 0
+
+ phosphorylation with prompt loss on Y
+ -18.010565
+ -18.0153
+ 0
+
+ Y
+
+ 23
+ Dehydrated
+
+
+
+ 99
+
+
+ 0
+
+ phosphorylation with neutral loss on C
+ 79.966331
+ 79.9799
+ 0
+
+ C
+
+
+
+ 97.976896
+ 97.9952
+ 0
+
+
+ 21
+ Phospho
+
+
+
+ 100
+
+
+ 0
+
+ phosphorylation with neutral loss on D
+ 79.966331
+ 79.9799
+ 0
+
+ D
+
+
+
+ 97.976896
+ 97.9952
+ 0
+
+
+ 21
+ Phospho
+
+
+
+ 101
+
+
+ 0
+
+ phosphorylation with neutral loss on H
+ 79.966331
+ 79.9799
+ 0
+
+ H
+
+
+
+ 97.976896
+ 97.9952
+ 0
+
+
+ 21
+ Phospho
+
+
+
+ 102
+
+
+ 0
+
+ propionyl light K
+ 56.026215
+ 56.0633
+ 0
+
+ K
+
+ 58
+ Propionyl
+
+
+
+ 103
+
+
+ 5
+
+ propionyl light on peptide n-term
+ 56.026215
+ 56.0633
+ 0
+ 58
+ Propionyl
+
+
+
+ 104
+
+
+ 0
+
+ propionyl heavy K
+ 59.036279
+ 59.0412
+ 0
+
+ K
+
+ 59
+ Propionyl:13C(3)
+
+
+
+ 105
+
+
+ 5
+
+ propionyl heavy peptide n-term
+ 59.036279
+ 59.0412
+ 0
+ 59
+ Propionyl:13C(3)
+
+
+
+ 106
+
+
+ 0
+
+ pyridyl K
+ 119.037114
+ 119.1207
+ 0
+
+ K
+
+ 25
+ Pyridylacetyl
+
+
+
+ 107
+
+
+ 5
+
+ pyridyl peptide n-term
+ 119.037114
+ 119.1207
+ 0
+ 25
+ Pyridylacetyl
+
+
+
+ 108
+
+
+ 6
+
+ pyro-cmC
+ -17.026549
+ -17.0305
+ 0
+
+ C
+
+ 385
+ Ammonia-loss
+
+
+
+ 109
+
+
+ 6
+
+ pyro-glu from n-term E
+ -18.010565
+ -18.0153
+ 0
+
+ E
+
+ 27
+ Glu->pyro-Glu
+
+
+
+ 110
+
+
+ 6
+
+ pyro-glu from n-term Q
+ -17.026549
+ -17.0305
+ 0
+
+ Q
+
+ 385
+ Ammonia-loss
+
+
+
+ 111
+
+
+ 0
+
+ oxidation of P to pyroglutamic acid
+ 13.979265
+ 13.9835
+ 0
+
+ P
+
+ 359
+ Pro->pyro-Glu
+
+
+
+ 112
+
+
+ 0
+
+ s-pyridylethylation of C
+ 105.057849
+ 105.1372
+ 0
+
+ C
+
+ 31
+ Pyridylethyl
+
+
+
+ 113
+
+
+ 0
+
+ SeMet
+ 47.944449
+ 46.8950
+ 0
+
+ M
+
+ 162
+ Delta:S(-1)Se(1)
+
+
+
+ 114
+
+
+ 0
+
+ sulfation of Y
+ 79.956815
+ 80.0632
+ 0
+
+ Y
+
+ 40
+ Sulfo
+
+
+
+ 115
+
+
+ 0
+
+ sulphone of M
+ 31.989829
+ 31.9988
+ 0
+
+ M
+
+ 425
+ Dioxidation
+
+
+
+ 116
+
+
+ 0
+
+ tri-iodination of Y
+ 377.689944
+ 377.6896
+ 0
+
+ Y
+
+ 131
+ Triiodo
+
+
+
+ 117
+
+
+ 0
+
+ tri-methylation of R
+ 42.046950
+ 42.0797
+ 0
+
+ R
+
+ 37
+ Trimethyl
+
+
+
+ 118
+
+
+ 6
+
+ n-acyl diglyceride cysteine
+ 788.725777
+ 789.3049
+ 0
+
+ C
+
+ 51
+ Tripalmitate
+
+
+
+ 129
+
+
+ 0
+
+ ICAT light
+ 227.126991
+ 227.2603
+ 0
+
+ C
+
+ 105
+ ICAT-C
+
+
+
+ 130
+
+
+ 0
+
+ ICAT heavy
+ 236.157185
+ 236.1942
+ 0
+
+ C
+
+ 106
+ ICAT-C:13C(9)
+
+
+
+ 131
+
+
+ 0
+
+ CAMthiopropanoyl K
+ 145.019749
+ 145.1796
+ 0
+
+ K
+
+ 293
+ CAMthiopropanoyl
+
+
+
+ 132
+
+
+ 0
+
+ phosphorylation with neutral loss on S
+ 79.966331
+ 79.9799
+ 0
+
+ S
+
+
+
+ 97.976896
+ 97.9952
+ 0
+
+
+ 21
+ Phospho
+
+
+
+ 133
+
+
+ 0
+
+ phosphorylation with neutral loss on T
+ 79.966331
+ 79.9799
+ 0
+
+ T
+
+
+
+ 97.976896
+ 97.9952
+ 0
+
+
+ 21
+ Phospho
+
+
+
+ 134
+
+
+ 0
+
+ phosphorylation of S with ETD loss
+ 79.966331
+ 79.9799
+ 0
+
+ S
+
+
+
+ 2.016
+ 2.016
+ 0
+
+
+
+
+
+ 135
+
+
+ 0
+
+ phosphorylation of T with ETD loss
+ 79.966331
+ 79.9799
+ 0
+
+ T
+
+
+
+ 2.016
+ 2.016
+ 0
+
+
+
+
+
+ 136
+
+
+ 0
+
+ heavy arginine-13C6
+ 6.020129
+ 5.9559
+ 0
+
+ R
+
+ 188
+ Label:13C(6)
+
+
+
+ 137
+
+
+ 0
+
+ heavy arginine-13C6-15N4
+ 10.008269
+ 9.9296
+ 0
+
+ R
+
+ 267
+ Label:13C(6)15N(4)
+
+
+
+ 138
+
+
+ 0
+
+ heavy lysine-13C6
+ 6.020129
+ 5.9559
+ 0
+
+ K
+
+ 188
+ Label:13C(6)
+
+
+
+ 139
+
+
+ 6
+
+ PNGasF in O18 water
+ 2.988261
+ 2.9845
+ 0
+
+ N
+
+ 366
+ Deamidated:18O(1)
+
+
+
+ 140
+
+
+ 0
+
+ beta elimination of S
+ -18.010565
+ -18.0153
+ 0
+
+ S
+
+ 23
+ Dehydrated
+
+
+
+ 141
+
+
+ 0
+
+ beta elimination of T
+ -18.010565
+ -18.0153
+ 0
+
+ T
+
+ 23
+ Dehydrated
+
+
+
+ 162
+
+
+ 0
+
+ oxidation of C to sulfinic acid
+ 31.989829
+ 31.9988
+ 0
+
+ C
+
+ 425
+ Dioxidation
+
+
+
+ 163
+
+
+ 0
+
+ arginine to ornithine
+ -42.021798
+ -42.0400
+ 0
+
+ R
+
+ 372
+ Arg->Orn
+
+
+
+ 164
+
+
+ 0
+
+ dehydro of S and T
+ -18.010565
+ -18.0153
+ 0
+
+ S
+ T
+
+ 23
+ Dehydrated
+
+
+
+ 165
+
+
+ 0
+
+ carboxykynurenin of W
+ 47.98474389
+ 47.9979141
+ 0
+
+ W
+
+
+
+
+ 166
+
+
+ 0
+
+ sumoylation of K
+ 484.2282
+ 0
+ 0
+
+ K
+
+ 846
+
+
+
+ 167
+
+
+ 5
+
+ iTRAQ114 on nterm
+ 144.105918
+ 144.1680
+ 0
+ 532
+ iTRAQ4plex114
+
+
+
+ 168
+
+
+ 0
+
+ iTRAQ114 on K
+ 144.105918
+ 144.1680
+ 0
+
+ K
+
+ 532
+ iTRAQ4plex114
+
+
+
+ 169
+
+
+ 0
+
+ iTRAQ114 on Y
+ 144.105918
+ 144.1680
+ 0
+
+ Y
+
+ 532
+ iTRAQ4plex114
+
+
+
+ 170
+
+
+ 5
+
+ iTRAQ115 on nterm
+ 144.099599
+ 144.1688
+ 0
+ 533
+ iTRAQ4plex115
+
+
+
+ 171
+
+
+ 0
+
+ iTRAQ115 on K
+ 144.099599
+ 144.1688
+ 0
+
+ K
+
+ 533
+ iTRAQ4plex115
+
+
+
+ 172
+
+
+ 0
+
+ iTRAQ115 on Y
+ 144.099599
+ 144.1688
+ 0
+
+ Y
+
+ 533
+ iTRAQ4plex115
+
+
+
+ 173
+
+
+ 5
+
+ iTRAQ116 on nterm
+ 144.102063
+ 144.1544
+ 0
+ 214
+ iTRAQ4plex
+
+
+
+ 174
+
+
+ 0
+
+ iTRAQ116 on K
+ 144.102063
+ 144.1544
+ 0
+
+ K
+
+ 214
+ iTRAQ4plex
+
+
+
+ 175
+
+
+ 0
+
+ iTRAQ116 on Y
+ 144.102063
+ 144.1544
+ 0
+
+ Y
+
+ 214
+ iTRAQ4plex
+
+
+
+ 176
+
+
+ 5
+
+ iTRAQ117 on nterm
+ 144.102063
+ 144.1544
+ 0
+ 214
+ iTRAQ4plex
+
+
+
+ 177
+
+
+ 0
+
+ iTRAQ117 on K
+ 144.102063
+ 144.1544
+ 0
+
+ K
+
+ 214
+ iTRAQ4plex
+
+
+
+ 178
+
+
+ 0
+
+ iTRAQ117 on Y
+ 144.102063
+ 144.1544
+ 0
+
+ Y
+
+ 214
+ iTRAQ4plex
+
+
+
+ 179
+
+
+ 0
+
+ MMTS on C
+ 45.987721
+ 46.0916
+ 0
+
+ C
+
+ 39
+ Methylthio
+
+
+
+ 180
+
+
+ 0
+
+ heavy lysine - 2H4
+ 4.025107
+ 4.0246
+ 0
+
+ K
+
+ 481
+ Label:2H(4)
+
+
+
+ 181
+
+
+ 0
+
+ heavy lysine - 13C6 15N2
+ 8.014199
+ 7.9427
+ 0
+
+ K
+
+ 259
+ Label:13C(6)15N(2)
+
+
+
+ 182
+
+
+ 0
+
+ Asparagine HexNAc
+ 203.079373
+ 203.1925
+ 0
+
+ N
+
+ 43
+ HexNAc
+
+
+
+ 183
+
+
+ 0
+
+ Asparagine dHexHexNAc
+ 349.137281
+ 349.3337
+ 0
+
+ N
+
+ 142
+ HexNAc(1)dHex(1)
+
+
+
+ 184
+
+
+ 0
+
+ Serine HexNAc
+ 203.079373
+ 203.1925
+ 0
+
+ S
+
+ 43
+ HexNAc
+
+
+
+ 185
+
+
+ 0
+
+ Threonine HexNAc
+ 203.079373
+ 203.1925
+ 0
+
+ T
+
+ 43
+ HexNAc
+
+
+
+ 186
+
+
+ 0
+
+ palmitoleyl of S
+ 236.214016
+ 236.3929
+ 0
+
+ S
+
+ 431
+ Palmitoleyl
+
+
+
+ 187
+
+
+ 0
+
+ palmitoleyl of C
+ 236.214016
+ 236.3929
+ 0
+
+ C
+
+ 431
+ Palmitoleyl
+
+
+
+ 188
+
+
+ 0
+
+ palmitoleyl of T
+ 236.214016
+ 236.3929
+ 0
+
+ T
+
+ 431
+ Palmitoleyl
+
+
+
+ 189
+
+
+ 0
+
+ CHD2-di-methylation of K
+ 32.056407
+ 32.0778
+ 0
+
+ K
+
+ 199
+ Dimethyl:2H(4)
+
+
+
+ 190
+
+
+ 5
+
+ CHD2-di-methylation of peptide n-term
+ 32.056407
+ 32.0778
+ 0
+ 199
+ Dimethyl:2H(4)
+
+
+
+ 191
+
+
+ 0
+
+ Maleimide-PEO2-Biotin of C
+ 525.225719
+ 525.6183
+ 0
+
+ C
+
+ 522
+ Maleimide-PEO2-Biotin
+
+
+
+ 192
+
+
+ 0
+
+ phosphorylation of H
+ 79.966331
+ 79.9799
+ 0
+
+ H
+
+ 21
+ Phospho
+
+
+
+ 193
+
+
+ 0
+
+ oxidation of C
+ 15.994915
+ 15.9994
+ 0
+
+ C
+
+ 35
+ Oxidation
+
+
+
+ 194
+
+
+ 0
+
+ oxidation of Y (duplicate of 64)
+ 15.994915
+ 15.9994
+ 0
+
+ Y
+
+ 35
+ Oxidation
+
+
+
+ 195
+
+
+ 0
+
+ Uniblue A on K
+ 484.039891
+ 484.5016
+ 0
+
+ K
+
+
+
+
+ 196
+
+
+ 0
+
+ deamidation of N
+ 0.984016
+ 0.9848
+ 0
+
+ N
+
+ 7
+ Deamidated
+
+
+
+ 197
+
+
+ 0
+
+ trideuteration of L (SILAC)
+ 3.018830
+ 3.0185
+ 0
+
+ L
+
+ 262
+ Label:2H(3)
+
+
+
+ 198
+
+
+ 0
+
+ TMT duplex on K
+ 225.155833
+ 225.2921
+ 0
+
+ K
+
+ 738
+
+
+
+ 199
+
+
+ 5
+
+ TMT duplex on n-term peptide
+ 225.155833
+ 225.2921
+ 0
+
+ X
+
+ 738
+
+
+
+ 198
+
+
+ 0
+
+ TMT 6-plex on K
+ 229.162932
+ 229.2634
+ 0
+
+ K
+
+ 738
+
+
+
+ 199
+
+
+ 5
+
+ TMT 6-plex on n-term peptide
+ 229.162932
+ 229.2634
+ 0
+
+ X
+
+ 738
+
+
+
+ 200
+
+
+ 5
+
+ iTRAQ8plex:13C(7)15N(1) on nterm
+ 304.205360
+ 304.3074
+ 0
+ 730
+
+
+
+ 201
+
+
+ 0
+
+ iTRAQ8plex:13C(7)15N(1) on K
+ 304.205360
+ 304.3074
+ 0
+
+ K
+
+ 730
+
+
+
+ 202
+
+
+ 0
+
+ iTRAQ8plex:13C(7)15N(1) on Y
+ 304.205360
+ 304.3074
+ 0
+
+ Y
+
+ 730
+
+
+
+ 203
+
+
+ 5
+
+ iTRAQ8plex:13C(6)15N(2) on nterm
+ 304.199040
+ 304.3081
+ 0
+ 731
+
+
+
+ 204
+
+
+ 0
+
+ iTRAQ8plex:13C(6)15N(2) on K
+ 304.199040
+ 304.3081
+ 0
+
+ K
+
+ 731
+
+
+
+ 205
+
+
+ 0
+
+ iTRAQ8plex:13C(6)15N(2) on Y
+ 304.199040
+ 304.3081
+ 0
+
+ Y
+
+ 731
+
+
+
+ 206
+
+
+ 0
+
+ selenocysteine
+ 47.944449
+ 46.8950
+ 0
+
+ C
+
+ 162
+
+
+
+ 207
+
+
+ 0
+
+ carboxymethylated selenocysteine
+ 105.949928
+ 104.9311
+ 0
+
+ C
+
+
+
diff -r 000000000000 -r 0578e296cab4 searchGUI_usermods.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/searchGUI_usermods.xml Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,455 @@
+
+
+
+
+
+ 119
+
+
+ 5
+
+ dimethyl 2d n-terminus
+ 32.0564
+ 0
+ 0
+
+
+
+ 120
+
+
+ 0
+
+ dimethyl 2d k
+ 32.0564
+ 0
+ 0
+
+ K
+
+
+
+
+ 121
+
+
+ 0
+
+ gtp desthiobiotinc12
+ 196.121178
+ 0
+ 0
+
+ K
+
+
+
+
+ 122
+
+
+ 0
+
+ gtp desthiobiotinc13
+ 202.141307
+ 0
+ 0
+
+ K
+
+
+
+
+ 123
+
+
+ 0
+
+ User modification 5
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 124
+
+
+ 0
+
+ User modification 6
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 125
+
+
+ 0
+
+ User modification 7
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 126
+
+
+ 0
+
+ User modification 8
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 127
+
+
+ 0
+
+ User modification 9
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 128
+
+
+ 0
+
+ User modification 10
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 142
+
+
+ 0
+
+ User modification 11
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 143
+
+
+ 0
+
+ User modification 12
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 144
+
+
+ 0
+
+ User modification 13
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 145
+
+
+ 0
+
+ User modification 14
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 146
+
+
+ 0
+
+ User modification 15
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 147
+
+
+ 0
+
+ User modification 16
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 148
+
+
+ 0
+
+ User modification 17
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 149
+
+
+ 0
+
+ User modification 18
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 150
+
+
+ 0
+
+ User modification 19
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 151
+
+
+ 0
+
+ User modification 20
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 152
+
+
+ 0
+
+ User modification 21
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 153
+
+
+ 0
+
+ User modification 22
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 154
+
+
+ 0
+
+ User modification 23
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 155
+
+
+ 0
+
+ User modification 24
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 156
+
+
+ 0
+
+ User modification 25
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 157
+
+
+ 0
+
+ User modification 26
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 158
+
+
+ 0
+
+ User modification 27
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 159
+
+
+ 0
+
+ User modification 28
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 160
+
+
+ 0
+
+ User modification 29
+ 0
+ 0
+ 0
+
+ X
+
+
+
+
+ 161
+
+
+ 0
+
+ User modification 30
+ 0
+ 0
+ 0
+
+ X
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 0578e296cab4 searchgui_mods.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/searchgui_mods.loc Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,210 @@
+methylation of k
+oxidation of m
+carboxymethyl c
+carbamidomethyl c
+deamidation of n and q
+propionamide c
+phosphorylation of s
+phosphorylation of t
+phosphorylation of y
+m cleavage from protein n-term
+acetylation of protein n-term
+methylation of protein n-term
+tri-methylation of protein n-term
+beta methythiolation of d
+methylation of q
+tri-methylation of k
+methylation of d
+methylation of e
+methylation of peptide c-term
+tri-deuteromethylation of d
+tri-deuteromethylation of e
+tri-deuteromethylation of peptide c-term
+n-formyl met addition
+2-amino-3-oxo-butanoic acid t
+acetylation of k
+amidation of peptide c-term
+beta-methylthiolation of d (duplicate of 13)
+carboxyamidomethylation of k
+carboxyamidomethylation of h
+carboxyamidomethylation of d
+carboxyamidomethylation of e
+carbamylation of k
+carbamylation of n-term peptide
+citrullination of r
+oxidation of c to cysteic acid
+di-iodination of y
+di-methylation of k
+di-methylation of r
+di-methylation of peptide n-term
+oxidation of f to dihydroxyphenylalanine
+gammathiopropionylation of k
+gammathiopropionylation of peptide n-term
+farnesylation of c
+formylation of k
+formylation of peptide n-term
+oxidation of w to formylkynurenin
+fluorophenylalanine
+beta-carboxylation of d
+gamma-carboxylation of e
+geranyl-geranyl
+glucuronylation of protein n-term
+glutathione disulfide
+ubiquitinylation residue
+guanidination of k
+oxidation of h to n
+oxidation of h to d
+homoserine
+homoserine lactone
+oxidation of w to hydroxykynurenin
+hydroxylation of d
+hydroxylation of k
+hydroxylation of n
+hydroxylation of p
+hydroxylation of f
+hydroxylation of y
+iodination of y
+oxidation of w to kynurenin
+lipoyl k
+methyl ester of peptide c-term (duplicate of 18)
+methyl ester of d
+methyl ester of e (duplicate of 17)
+methyl ester of s
+methyl ester of y
+methyl c
+methyl h
+methyl n
+methylation of peptide n-term
+methyl r
+myristoleylation of g
+myristoyl-4h of g
+myristoylation of peptide n-term g
+myristoylation of k
+formylation of protein n-term
+nem c
+nipcam
+oxidation of w to nitro
+oxidation of y to nitro
+o18 on peptide n-term
+di-o18 on peptide n-term
+oxidation of h
+oxidation of w
+phosphopantetheine s
+palmitoylation of c
+palmitoylation of k
+palmitoylation of s
+palmitoylation of t
+phosphorylation of s with prompt loss
+phosphorylation of t with prompt loss
+phosphorylation with prompt loss on y
+phosphorylation with neutral loss on c
+phosphorylation with neutral loss on d
+phosphorylation with neutral loss on h
+propionyl light k
+propionyl light on peptide n-term
+propionyl heavy k
+propionyl heavy peptide n-term
+pyridyl k
+pyridyl peptide n-term
+pyro-cmc
+pyro-glu from n-term e
+pyro-glu from n-term q
+oxidation of p to pyroglutamic acid
+s-pyridylethylation of c
+semet
+sulfation of y
+sulphone of m
+tri-iodination of y
+tri-methylation of r
+n-acyl diglyceride cysteine
+icat light
+icat heavy
+camthiopropanoyl k
+phosphorylation with neutral loss on s
+phosphorylation with neutral loss on t
+phosphorylation of s with etd loss
+phosphorylation of t with etd loss
+heavy arginine-13c6
+heavy arginine-13c6-15n4
+heavy lysine-13c6
+pngasf in o18 water
+beta elimination of s
+beta elimination of t
+oxidation of c to sulfinic acid
+arginine to ornithine
+dehydro of s and t
+carboxykynurenin of w
+sumoylation of k
+itraq114 on nterm
+itraq114 on k
+itraq114 on y
+itraq115 on nterm
+itraq115 on k
+itraq115 on y
+itraq116 on nterm
+itraq116 on k
+itraq116 on y
+itraq117 on nterm
+itraq117 on k
+itraq117 on y
+mmts on c
+heavy lysine - 2h4
+heavy lysine - 13c6 15n2
+asparagine hexnac
+asparagine dhexhexnac
+serine hexnac
+threonine hexnac
+palmitoleyl of s
+palmitoleyl of c
+palmitoleyl of t
+chd2-di-methylation of k
+chd2-di-methylation of peptide n-term
+maleimide-peo2-biotin of c
+phosphorylation of h
+oxidation of c
+oxidation of y (duplicate of 64)
+uniblue a on k
+deamidation of n
+trideuteration of l (silac)
+tmt duplex on k
+tmt duplex on n-term peptide
+tmt 6-plex on k
+tmt 6-plex on n-term peptide
+itraq8plex:13c(7)15n(1) on nterm
+itraq8plex:13c(7)15n(1) on k
+itraq8plex:13c(7)15n(1) on y
+itraq8plex:13c(6)15n(2) on nterm
+itraq8plex:13c(6)15n(2) on k
+itraq8plex:13c(6)15n(2) on y
+selenocysteine
+carboxymethylated selenocysteine
+dimethyl 2d n-terminus
+dimethyl 2d k
+gtp desthiobiotinc12
+gtp desthiobiotinc13
+user modification 5
+user modification 6
+user modification 7
+user modification 8
+user modification 9
+user modification 10
+user modification 11
+user modification 12
+user modification 13
+user modification 14
+user modification 15
+user modification 16
+user modification 17
+user modification 18
+user modification 19
+user modification 20
+user modification 21
+user modification 22
+user modification 23
+user modification 24
+user modification 25
+user modification 26
+user modification 27
+user modification 28
+user modification 29
+user modification 30
diff -r 000000000000 -r 0578e296cab4 searchgui_mods.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/searchgui_mods.loc.sample Fri May 10 17:58:22 2013 -0400
@@ -0,0 +1,210 @@
+methylation of k
+oxidation of m
+carboxymethyl c
+carbamidomethyl c
+deamidation of n and q
+propionamide c
+phosphorylation of s
+phosphorylation of t
+phosphorylation of y
+m cleavage from protein n-term
+acetylation of protein n-term
+methylation of protein n-term
+tri-methylation of protein n-term
+beta methythiolation of d
+methylation of q
+tri-methylation of k
+methylation of d
+methylation of e
+methylation of peptide c-term
+tri-deuteromethylation of d
+tri-deuteromethylation of e
+tri-deuteromethylation of peptide c-term
+n-formyl met addition
+2-amino-3-oxo-butanoic acid t
+acetylation of k
+amidation of peptide c-term
+beta-methylthiolation of d (duplicate of 13)
+carboxyamidomethylation of k
+carboxyamidomethylation of h
+carboxyamidomethylation of d
+carboxyamidomethylation of e
+carbamylation of k
+carbamylation of n-term peptide
+citrullination of r
+oxidation of c to cysteic acid
+di-iodination of y
+di-methylation of k
+di-methylation of r
+di-methylation of peptide n-term
+oxidation of f to dihydroxyphenylalanine
+gammathiopropionylation of k
+gammathiopropionylation of peptide n-term
+farnesylation of c
+formylation of k
+formylation of peptide n-term
+oxidation of w to formylkynurenin
+fluorophenylalanine
+beta-carboxylation of d
+gamma-carboxylation of e
+geranyl-geranyl
+glucuronylation of protein n-term
+glutathione disulfide
+ubiquitinylation residue
+guanidination of k
+oxidation of h to n
+oxidation of h to d
+homoserine
+homoserine lactone
+oxidation of w to hydroxykynurenin
+hydroxylation of d
+hydroxylation of k
+hydroxylation of n
+hydroxylation of p
+hydroxylation of f
+hydroxylation of y
+iodination of y
+oxidation of w to kynurenin
+lipoyl k
+methyl ester of peptide c-term (duplicate of 18)
+methyl ester of d
+methyl ester of e (duplicate of 17)
+methyl ester of s
+methyl ester of y
+methyl c
+methyl h
+methyl n
+methylation of peptide n-term
+methyl r
+myristoleylation of g
+myristoyl-4h of g
+myristoylation of peptide n-term g
+myristoylation of k
+formylation of protein n-term
+nem c
+nipcam
+oxidation of w to nitro
+oxidation of y to nitro
+o18 on peptide n-term
+di-o18 on peptide n-term
+oxidation of h
+oxidation of w
+phosphopantetheine s
+palmitoylation of c
+palmitoylation of k
+palmitoylation of s
+palmitoylation of t
+phosphorylation of s with prompt loss
+phosphorylation of t with prompt loss
+phosphorylation with prompt loss on y
+phosphorylation with neutral loss on c
+phosphorylation with neutral loss on d
+phosphorylation with neutral loss on h
+propionyl light k
+propionyl light on peptide n-term
+propionyl heavy k
+propionyl heavy peptide n-term
+pyridyl k
+pyridyl peptide n-term
+pyro-cmc
+pyro-glu from n-term e
+pyro-glu from n-term q
+oxidation of p to pyroglutamic acid
+s-pyridylethylation of c
+semet
+sulfation of y
+sulphone of m
+tri-iodination of y
+tri-methylation of r
+n-acyl diglyceride cysteine
+icat light
+icat heavy
+camthiopropanoyl k
+phosphorylation with neutral loss on s
+phosphorylation with neutral loss on t
+phosphorylation of s with etd loss
+phosphorylation of t with etd loss
+heavy arginine-13c6
+heavy arginine-13c6-15n4
+heavy lysine-13c6
+pngasf in o18 water
+beta elimination of s
+beta elimination of t
+oxidation of c to sulfinic acid
+arginine to ornithine
+dehydro of s and t
+carboxykynurenin of w
+sumoylation of k
+itraq114 on nterm
+itraq114 on k
+itraq114 on y
+itraq115 on nterm
+itraq115 on k
+itraq115 on y
+itraq116 on nterm
+itraq116 on k
+itraq116 on y
+itraq117 on nterm
+itraq117 on k
+itraq117 on y
+mmts on c
+heavy lysine - 2h4
+heavy lysine - 13c6 15n2
+asparagine hexnac
+asparagine dhexhexnac
+serine hexnac
+threonine hexnac
+palmitoleyl of s
+palmitoleyl of c
+palmitoleyl of t
+chd2-di-methylation of k
+chd2-di-methylation of peptide n-term
+maleimide-peo2-biotin of c
+phosphorylation of h
+oxidation of c
+oxidation of y (duplicate of 64)
+uniblue a on k
+deamidation of n
+trideuteration of l (silac)
+tmt duplex on k
+tmt duplex on n-term peptide
+tmt 6-plex on k
+tmt 6-plex on n-term peptide
+itraq8plex:13c(7)15n(1) on nterm
+itraq8plex:13c(7)15n(1) on k
+itraq8plex:13c(7)15n(1) on y
+itraq8plex:13c(6)15n(2) on nterm
+itraq8plex:13c(6)15n(2) on k
+itraq8plex:13c(6)15n(2) on y
+selenocysteine
+carboxymethylated selenocysteine
+dimethyl 2d n-terminus
+dimethyl 2d k
+gtp desthiobiotinc12
+gtp desthiobiotinc13
+user modification 5
+user modification 6
+user modification 7
+user modification 8
+user modification 9
+user modification 10
+user modification 11
+user modification 12
+user modification 13
+user modification 14
+user modification 15
+user modification 16
+user modification 17
+user modification 18
+user modification 19
+user modification 20
+user modification 21
+user modification 22
+user modification 23
+user modification 24
+user modification 25
+user modification 26
+user modification 27
+user modification 28
+user modification 29
+user modification 30
diff -r 000000000000 -r 0578e296cab4 update.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh Fri May 10 17:58:22 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