divvy_proteomics 0.0.1
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- data/.document +5 -0
- data/.rspec +1 -0
- data/Gemfile +13 -0
- data/LICENSE.txt +20 -0
- data/README.md +45 -0
- data/Rakefile +49 -0
- data/VERSION +1 -0
- data/bin/divvy_spectra +362 -0
- data/divvy_proteomics.gemspec +74 -0
- data/lib/divvy_proteomics.rb +0 -0
- data/spec/data/merge_definition.csv +1 -0
- data/spec/data/multiply_mapped_spectra.csv +95 -0
- data/spec/data/single_protein.csv +52 -0
- data/spec/data/single_protein_with_aliases.csv +53 -0
- data/spec/data/three_proteins.csv +76 -0
- data/spec/data/three_proteins_meant_for_merge.csv +81 -0
- data/spec/data/three_proteins_with_contaminant.csv +87 -0
- data/spec/divvy_proteomics_spec.rb +106 -0
- data/spec/spec_helper.rb +12 -0
- metadata +166 -0
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# Generated by jeweler
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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Gem::Specification.new do |s|
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s.name = "divvy_proteomics"
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s.version = "0.0.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Ben J Woodcroft"]
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s.date = "2013-04-13"
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s.description = "divvy up spectra from DTASelect files in a somewhat parsimonious way"
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s.email = "donttrustben@gmail.com"
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s.executables = ["divvy_spectra"]
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s.extra_rdoc_files = [
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"LICENSE.txt",
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"README.md"
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]
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s.files = [
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".document",
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".rspec",
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"Gemfile",
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"LICENSE.txt",
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"README.md",
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"Rakefile",
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"VERSION",
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"bin/divvy_spectra",
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"divvy_proteomics.gemspec",
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"lib/divvy_proteomics.rb",
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"spec/data/merge_definition.csv",
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"spec/data/multiply_mapped_spectra.csv",
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"spec/data/single_protein.csv",
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"spec/data/single_protein_with_aliases.csv",
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"spec/data/three_proteins.csv",
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"spec/data/three_proteins_meant_for_merge.csv",
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"spec/data/three_proteins_with_contaminant.csv",
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"spec/divvy_proteomics_spec.rb",
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"spec/spec_helper.rb"
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]
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s.homepage = "http://github.com/wwood/divvy_proteomics"
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s.licenses = ["MIT"]
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s.require_paths = ["lib"]
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s.rubygems_version = "1.8.24"
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s.summary = "divvy up spectra from DTASelect files in a parsimonious way"
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if s.respond_to? :specification_version then
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s.specification_version = 3
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if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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s.add_runtime_dependency(%q<bio-logger>, [">= 0"])
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s.add_development_dependency(%q<systemu>, [">= 0"])
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s.add_development_dependency(%q<rspec>, [">= 2.8.0"])
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s.add_development_dependency(%q<rdoc>, [">= 3.12"])
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s.add_development_dependency(%q<bundler>, [">= 1.0.0"])
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s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
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else
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s.add_dependency(%q<bio-logger>, [">= 0"])
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s.add_dependency(%q<systemu>, [">= 0"])
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s.add_dependency(%q<rspec>, [">= 2.8.0"])
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s.add_dependency(%q<rdoc>, [">= 3.12"])
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s.add_dependency(%q<bundler>, [">= 1.0.0"])
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s.add_dependency(%q<jeweler>, [">= 1.8.4"])
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end
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else
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s.add_dependency(%q<bio-logger>, [">= 0"])
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s.add_dependency(%q<systemu>, [">= 0"])
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s.add_dependency(%q<rspec>, [">= 2.8.0"])
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s.add_dependency(%q<rdoc>, [">= 3.12"])
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s.add_dependency(%q<bundler>, [">= 1.0.0"])
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s.add_dependency(%q<jeweler>, [">= 1.8.4"])
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end
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end
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File without changes
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eDeep20120820:eD1_1639_1 eDeep20120820:eD1_1639_1_merge
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DTASelect v1.9
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/auto/gtl/ms/Abisko_Soils/Field_Sampling_Aug_2010/SurfDeep/Erio_Deep_Aug2010_27Jun_TR1/Frac1/analysis/tryp_edeep_20120820_Mstor4.3.2/sequest
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/auto/gtl/db/Abisko_Soils/edeep_20120820_Mstor4.3.2_cntm_psm
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SEQUEST v.27 in SQT format.
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--DB -p 2 -r 1000
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true Use criteria
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1.8 Minimum +1 XCorr
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2.5 Minimum +2 XCorr
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3.5 Minimum +3 XCorr
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0.08 Minimum DeltCN
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1 Minimum charge state
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3 Maximum charge state
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0 Minimum ion proportion
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1000 Maximum Sp rank
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-1 Minimum Sp score
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Include Modified peptide inclusion
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Any Tryptic status requirement
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true Multiple, ambiguous IDs allowed
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Ignore Peptide validation handling
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XCorr Purge duplicate peptides by protein
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false Include only loci with unique peptide
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false Remove subset proteins
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Ignore Locus validation handling
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0 Minimum modified peptides per locus
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1000 Minimum redundancy for low coverage loci
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2 Minimum peptides per locus
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Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name
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Unique FileName XCorr DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence
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Mstor_v4.3.2:1344 15 188 58.6% 249 27617 8.7 U Methanoflorens_stordalmirensis_v4.3.2_01361 Methyl-coenzyme M reductase I subunit gamma
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20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
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20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05321.05321.1 1.8605 0.2699 822.3913 822.9573 3293.9 1 262 75 2 R.SWMAATR.F
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20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
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20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15208.15208.2 4.339 0.4065 1384.6218 1385.5929 6844.7 1 2135.8 90.9 35 K.MLLESEAFDCAR.S
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20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
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20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
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20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
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20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
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20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
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20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
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20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
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20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
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20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
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eDeep20120820:eD1_8237_2 16 220 57.4% 249 27683 8.9 U methyl-coenzyme M reductase gamma subunit # pI:8.94 MW:27683
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20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
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20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
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20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
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20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.14095.14095.2 4.8369 0.5277 1378.6663 1379.5707 9283.7 1 2692.6 90.9 56 K.MLLESEAFDPAR.S
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.13949.13949.1 2.4766 0.354 1380.67 1379.5707 4485.8 1 506.7 68.2 4 K.MLLESEAFDPAR.S
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_04.14749.14749.2 3.3302 0.2608 1777.8914 1779.0209 3944.1 8 231.6 46.7 9 K.MLLESEAFDPARSGVR.G
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20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
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20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
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20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
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20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
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20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
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20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
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20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
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20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
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20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
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eDeep20120820:eD1_1639_1 6 47 54.6% 97 10181 9.2 U chaperonin GroEL # pI:9.22 MW:10181
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_07.14607.14607.2 3.3369 0.4724 1576.8171 1577.8976 6120.3 1 1543.2 82.1 3 K.MANLGAQMVKEVASK.T
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.24627.24627.3 3.69 0.2962 2983.4954 2982.231 9369.6 1 1286.9 28.4 1 K.EVASKTSDVAGDGTTTATVLAQAIFNEGAR.L
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25402.25402.3 6.2951 0.4542 2466.2097 2467.6519 9066.5 1 4083.4 49 12 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25380.25380.2 5.5921 0.5669 2466.2104 2467.6519 7538.4 1 2687 64.6 4 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_02.08539.08539.2 3.2291 0.3305 1215.6385 1216.4381 4640.6 1 1013.9 77.3 4 R.LVAAGSNPMDIK.R
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_07.07029.07029.2 3.8934 0.3124 1371.7393 1372.6256 5850.5 1 1132.1 83.3 23 R.LVAAGSNPMDIKR.G
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eDeep20120820:eD1_13975_5 5 10 46.5% 114 12040 7.3 U chaperonin GroEL # pI:6.58 MW:12040
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2 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.03309.03309.1 2.2351 0.0941 701.4238 701.8412 3692.5 1 411.8 80 1 R.NVVIEK.S
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_06.10382.10382.2 3.3094 0.1685 1646.875 1647.8687 5179.8 1 1198.5 73.3 5 K.SWGSPTITKDGVTVAK.E
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_06.08631.08631.2 2.5536 0.1194 1166.6727 1164.3678 4460.4 6 699 77.8 1 K.FQNLGAQMVR.E
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25422.25422.2 3.6846 0.5519 2094.0518 2096.3018 5841.8 1 1462.4 70 2 K.TSDVAGDGTTTATVLAQAIFR.E
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25396.25396.3 3.7222 0.4465 2095.061 2096.3018 6365.6 1 1294.9 40 1 K.TSDVAGDGTTTATVLAQAIFR.E
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eDeep20120820:eD1_3396_1 5 39 45.0% 60 6451 9.7 U TGroEL # pI:9.70 MW:6451
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15191.15191.2 3.9035 0.3526 1595.925 1596.9138 3878.5 1 714 75 8 R.QAILRGVNKLADAVK.V
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.06178.06178.2 2.7941 0.1306 1014.557 1015.1979 4939.8 34 589.9 72.2 1 R.GVNKLADAVK.V
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.06181.06181.1 1.822 0.2189 1014.56 1015.1979 5053.4 16 231.5 50 1 R.GVNKLADAVK.V
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_08.17534.17534.2 4.7474 0.1538 1609.929 1610.9377 5966.2 1 1537.9 76.7 28 R.GVNKLADAVKVTLGPK.G
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2 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.03309.03309.1 2.2351 0.0941 701.4238 701.8412 3692.5 1 411.8 80 1 R.NVVLEK.K
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eDeep20120820:eD1_1494_8 6 11 15.7% 509 54101 5 U chaperonin GroEL # pI:4.93 MW:54101
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.16001.16001.2 2.8934 0.2246 1529.7815 1530.7393 4669.8 1 694.8 69.2 2 R.ALENGMNQLVDAVR.V
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2 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.03309.03309.1 2.2351 0.0941 701.4238 701.8412 3692.5 1 411.8 80 1 R.NVVLEK.K
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* 20120806_Erio_Deep_Aug2010_27Jun_TR1_11.06538.06538.2 3.0105 0.2342 1329.7216 1329.5602 6743.4 1 1215.2 83.3 2 R.NVAAGANPMSLKR.G
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*2 20120806_Erio_Deep_Aug2010_27Jun_TR1_02.06882.06882.2 2.7628 0.2128 843.5307 844.0421 3147.4 4 438.8 75 2 K.LSGGVAVIK.V
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+
20120806_Erio_Deep_Aug2010_27Jun_TR1_02.17582.17582.2 5.0532 0.1294 1607.9104 1608.8784 3425.9 1 1120.6 81.2 3 K.AAIEEGVVPGGGVALLR.A
|
|
88
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.13997.13997.2 4.9125 0.4921 2202.0728 2202.3396 9216.2 1 2282.2 67.5 1 R.AQQAILDAAEKLDDDEATGAR.I
|
|
89
|
+
Proteins Peptide IDs Copies
|
|
90
|
+
Unfiltered 93036 400116 424912
|
|
91
|
+
Redundant 390 1292 6998
|
|
92
|
+
Nonredundant 371 1094 5575
|
|
93
|
+
|
|
94
|
+
Classification Nonredundant Proteins Redundant Proteins
|
|
95
|
+
Unclassified 0 0
|
|
@@ -0,0 +1,52 @@
|
|
|
1
|
+
DTASelect v1.9
|
|
2
|
+
/auto/gtl/ms/Abisko_Soils/Field_Sampling_Aug_2010/SurfDeep/Erio_Deep_Aug2010_27Jun_TR1/Frac1/analysis/tryp_edeep_20120820_Mstor4.3.2/sequest
|
|
3
|
+
/auto/gtl/db/Abisko_Soils/edeep_20120820_Mstor4.3.2_cntm_psm
|
|
4
|
+
SEQUEST v.27 in SQT format.
|
|
5
|
+
--DB -p 2 -r 1000
|
|
6
|
+
true Use criteria
|
|
7
|
+
1.8 Minimum +1 XCorr
|
|
8
|
+
2.5 Minimum +2 XCorr
|
|
9
|
+
3.5 Minimum +3 XCorr
|
|
10
|
+
0.08 Minimum DeltCN
|
|
11
|
+
1 Minimum charge state
|
|
12
|
+
3 Maximum charge state
|
|
13
|
+
0 Minimum ion proportion
|
|
14
|
+
1000 Maximum Sp rank
|
|
15
|
+
-1 Minimum Sp score
|
|
16
|
+
Include Modified peptide inclusion
|
|
17
|
+
Any Tryptic status requirement
|
|
18
|
+
true Multiple, ambiguous IDs allowed
|
|
19
|
+
Ignore Peptide validation handling
|
|
20
|
+
XCorr Purge duplicate peptides by protein
|
|
21
|
+
false Include only loci with unique peptide
|
|
22
|
+
false Remove subset proteins
|
|
23
|
+
Ignore Locus validation handling
|
|
24
|
+
0 Minimum modified peptides per locus
|
|
25
|
+
1000 Minimum redundancy for low coverage loci
|
|
26
|
+
2 Minimum peptides per locus
|
|
27
|
+
|
|
28
|
+
Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name
|
|
29
|
+
Unique FileName XCorr DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence
|
|
30
|
+
Mstor_v4.3.2:1344 15 188 58.6% 249 27617 8.7 U Methanoflorens_stordalmirensis_v4.3.2_01361 Methyl-coenzyme M reductase I subunit gamma
|
|
31
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
32
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
33
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05321.05321.1 1.8605 0.2699 822.3913 822.9573 3293.9 1 262 75 2 R.SWMAATR.F
|
|
34
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
35
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
36
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15208.15208.2 4.339 0.4065 1384.6218 1385.5929 6844.7 1 2135.8 90.9 35 K.MLLESEAFDCAR.S
|
|
37
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
38
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
39
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
40
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
41
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
42
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
43
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
44
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
45
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
46
|
+
Proteins Peptide IDs Copies
|
|
47
|
+
Unfiltered 93036 400116 424912
|
|
48
|
+
Redundant 390 1292 6998
|
|
49
|
+
Nonredundant 371 1094 5575
|
|
50
|
+
|
|
51
|
+
Classification Nonredundant Proteins Redundant Proteins
|
|
52
|
+
Unclassified 0 0
|
|
@@ -0,0 +1,53 @@
|
|
|
1
|
+
DTASelect v1.9
|
|
2
|
+
/auto/gtl/ms/Abisko_Soils/Field_Sampling_Aug_2010/SurfDeep/Erio_Deep_Aug2010_27Jun_TR1/Frac1/analysis/tryp_edeep_20120820_Mstor4.3.2/sequest
|
|
3
|
+
/auto/gtl/db/Abisko_Soils/edeep_20120820_Mstor4.3.2_cntm_psm
|
|
4
|
+
SEQUEST v.27 in SQT format.
|
|
5
|
+
--DB -p 2 -r 1000
|
|
6
|
+
true Use criteria
|
|
7
|
+
1.8 Minimum +1 XCorr
|
|
8
|
+
2.5 Minimum +2 XCorr
|
|
9
|
+
3.5 Minimum +3 XCorr
|
|
10
|
+
0.08 Minimum DeltCN
|
|
11
|
+
1 Minimum charge state
|
|
12
|
+
3 Maximum charge state
|
|
13
|
+
0 Minimum ion proportion
|
|
14
|
+
1000 Maximum Sp rank
|
|
15
|
+
-1 Minimum Sp score
|
|
16
|
+
Include Modified peptide inclusion
|
|
17
|
+
Any Tryptic status requirement
|
|
18
|
+
true Multiple, ambiguous IDs allowed
|
|
19
|
+
Ignore Peptide validation handling
|
|
20
|
+
XCorr Purge duplicate peptides by protein
|
|
21
|
+
false Include only loci with unique peptide
|
|
22
|
+
false Remove subset proteins
|
|
23
|
+
Ignore Locus validation handling
|
|
24
|
+
0 Minimum modified peptides per locus
|
|
25
|
+
1000 Minimum redundancy for low coverage loci
|
|
26
|
+
2 Minimum peptides per locus
|
|
27
|
+
|
|
28
|
+
Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name
|
|
29
|
+
Unique FileName XCorr DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence
|
|
30
|
+
Mstor_v4.3.2:1344 15 188 58.6% 249 27617 8.7 U Methanoflorens_stordalmirensis_v4.3.2_01361 Methyl-coenzyme M reductase I subunit gamma
|
|
31
|
+
alias1 15 188 58.6% 249 27617 8.7 U alias1 Methyl-coenzyme M reductase I subunit gamma
|
|
32
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
33
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
34
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05321.05321.1 1.8605 0.2699 822.3913 822.9573 3293.9 1 262 75 2 R.SWMAATR.F
|
|
35
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
36
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
37
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15208.15208.2 4.339 0.4065 1384.6218 1385.5929 6844.7 1 2135.8 90.9 35 K.MLLESEAFDCAR.S
|
|
38
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
39
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
40
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
41
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
42
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
43
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
44
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
45
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
46
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
47
|
+
Proteins Peptide IDs Copies
|
|
48
|
+
Unfiltered 93036 400116 424912
|
|
49
|
+
Redundant 390 1292 6998
|
|
50
|
+
Nonredundant 371 1094 5575
|
|
51
|
+
|
|
52
|
+
Classification Nonredundant Proteins Redundant Proteins
|
|
53
|
+
Unclassified 0 0
|
|
@@ -0,0 +1,76 @@
|
|
|
1
|
+
DTASelect v1.9
|
|
2
|
+
/auto/gtl/ms/Abisko_Soils/Field_Sampling_Aug_2010/SurfDeep/Erio_Deep_Aug2010_27Jun_TR1/Frac1/analysis/tryp_edeep_20120820_Mstor4.3.2/sequest
|
|
3
|
+
/auto/gtl/db/Abisko_Soils/edeep_20120820_Mstor4.3.2_cntm_psm
|
|
4
|
+
SEQUEST v.27 in SQT format.
|
|
5
|
+
--DB -p 2 -r 1000
|
|
6
|
+
true Use criteria
|
|
7
|
+
1.8 Minimum +1 XCorr
|
|
8
|
+
2.5 Minimum +2 XCorr
|
|
9
|
+
3.5 Minimum +3 XCorr
|
|
10
|
+
0.08 Minimum DeltCN
|
|
11
|
+
1 Minimum charge state
|
|
12
|
+
3 Maximum charge state
|
|
13
|
+
0 Minimum ion proportion
|
|
14
|
+
1000 Maximum Sp rank
|
|
15
|
+
-1 Minimum Sp score
|
|
16
|
+
Include Modified peptide inclusion
|
|
17
|
+
Any Tryptic status requirement
|
|
18
|
+
true Multiple, ambiguous IDs allowed
|
|
19
|
+
Ignore Peptide validation handling
|
|
20
|
+
XCorr Purge duplicate peptides by protein
|
|
21
|
+
false Include only loci with unique peptide
|
|
22
|
+
false Remove subset proteins
|
|
23
|
+
Ignore Locus validation handling
|
|
24
|
+
0 Minimum modified peptides per locus
|
|
25
|
+
1000 Minimum redundancy for low coverage loci
|
|
26
|
+
2 Minimum peptides per locus
|
|
27
|
+
|
|
28
|
+
Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name
|
|
29
|
+
Unique FileName XCorr DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence
|
|
30
|
+
Mstor_v4.3.2:1344 15 188 58.6% 249 27617 8.7 U Methanoflorens_stordalmirensis_v4.3.2_01361 Methyl-coenzyme M reductase I subunit gamma
|
|
31
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
32
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
33
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05321.05321.1 1.8605 0.2699 822.3913 822.9573 3293.9 1 262 75 2 R.SWMAATR.F
|
|
34
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
35
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
36
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15208.15208.2 4.339 0.4065 1384.6218 1385.5929 6844.7 1 2135.8 90.9 35 K.MLLESEAFDCAR.S
|
|
37
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
38
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
39
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
40
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
41
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
42
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
43
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
44
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
45
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
46
|
+
eDeep20120820:eD1_8237_2 16 220 57.4% 249 27683 8.9 U methyl-coenzyme M reductase gamma subunit # pI:8.94 MW:27683
|
|
47
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
48
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
49
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
50
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
51
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.14095.14095.2 4.8369 0.5277 1378.6663 1379.5707 9283.7 1 2692.6 90.9 56 K.MLLESEAFDPAR.S
|
|
52
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.13949.13949.1 2.4766 0.354 1380.67 1379.5707 4485.8 1 506.7 68.2 4 K.MLLESEAFDPAR.S
|
|
53
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_04.14749.14749.2 3.3302 0.2608 1777.8914 1779.0209 3944.1 8 231.6 46.7 9 K.MLLESEAFDPARSGVR.G
|
|
54
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
55
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
56
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
57
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
58
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
59
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
60
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
61
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
62
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
63
|
+
eDeep20120820:eD1_1639_1 6 47 54.6% 97 10181 9.2 U chaperonin GroEL # pI:9.22 MW:10181
|
|
64
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_07.14607.14607.2 3.3369 0.4724 1576.8171 1577.8976 6120.3 1 1543.2 82.1 3 K.MANLGAQMVKEVASK.T
|
|
65
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.24627.24627.3 3.69 0.2962 2983.4954 2982.231 9369.6 1 1286.9 28.4 1 K.EVASKTSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
66
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25402.25402.3 6.2951 0.4542 2466.2097 2467.6519 9066.5 1 4083.4 49 12 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
67
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25380.25380.2 5.5921 0.5669 2466.2104 2467.6519 7538.4 1 2687 64.6 4 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
68
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_02.08539.08539.2 3.2291 0.3305 1215.6385 1216.4381 4640.6 1 1013.9 77.3 4 R.LVAAGSNPMDIK.R
|
|
69
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_07.07029.07029.2 3.8934 0.3124 1371.7393 1372.6256 5850.5 1 1132.1 83.3 23 R.LVAAGSNPMDIKR.G
|
|
70
|
+
Proteins Peptide IDs Copies
|
|
71
|
+
Unfiltered 93036 400116 424912
|
|
72
|
+
Redundant 390 1292 6998
|
|
73
|
+
Nonredundant 371 1094 5575
|
|
74
|
+
|
|
75
|
+
Classification Nonredundant Proteins Redundant Proteins
|
|
76
|
+
Unclassified 0 0
|
|
@@ -0,0 +1,81 @@
|
|
|
1
|
+
DTASelect v1.9
|
|
2
|
+
/auto/gtl/ms/Abisko_Soils/Field_Sampling_Aug_2010/SurfDeep/Erio_Deep_Aug2010_27Jun_TR1/Frac1/analysis/tryp_edeep_20120820_Mstor4.3.2/sequest
|
|
3
|
+
/auto/gtl/db/Abisko_Soils/edeep_20120820_Mstor4.3.2_cntm_psm
|
|
4
|
+
SEQUEST v.27 in SQT format.
|
|
5
|
+
--DB -p 2 -r 1000
|
|
6
|
+
true Use criteria
|
|
7
|
+
1.8 Minimum +1 XCorr
|
|
8
|
+
2.5 Minimum +2 XCorr
|
|
9
|
+
3.5 Minimum +3 XCorr
|
|
10
|
+
0.08 Minimum DeltCN
|
|
11
|
+
1 Minimum charge state
|
|
12
|
+
3 Maximum charge state
|
|
13
|
+
0 Minimum ion proportion
|
|
14
|
+
1000 Maximum Sp rank
|
|
15
|
+
-1 Minimum Sp score
|
|
16
|
+
Include Modified peptide inclusion
|
|
17
|
+
Any Tryptic status requirement
|
|
18
|
+
true Multiple, ambiguous IDs allowed
|
|
19
|
+
Ignore Peptide validation handling
|
|
20
|
+
XCorr Purge duplicate peptides by protein
|
|
21
|
+
false Include only loci with unique peptide
|
|
22
|
+
false Remove subset proteins
|
|
23
|
+
Ignore Locus validation handling
|
|
24
|
+
0 Minimum modified peptides per locus
|
|
25
|
+
1000 Minimum redundancy for low coverage loci
|
|
26
|
+
2 Minimum peptides per locus
|
|
27
|
+
|
|
28
|
+
Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name
|
|
29
|
+
Unique FileName XCorr DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence
|
|
30
|
+
Mstor_v4.3.2:1344 15 188 58.6% 249 27617 8.7 U Methanoflorens_stordalmirensis_v4.3.2_01361 Methyl-coenzyme M reductase I subunit gamma
|
|
31
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
32
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
33
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05321.05321.1 1.8605 0.2699 822.3913 822.9573 3293.9 1 262 75 2 R.SWMAATR.F
|
|
34
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
35
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
36
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15208.15208.2 4.339 0.4065 1384.6218 1385.5929 6844.7 1 2135.8 90.9 35 K.MLLESEAFDCAR.S
|
|
37
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
38
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
39
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
40
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
41
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
42
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
43
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
44
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
45
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
46
|
+
eDeep20120820:eD1_8237_2 16 220 57.4% 249 27683 8.9 U methyl-coenzyme M reductase gamma subunit # pI:8.94 MW:27683
|
|
47
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
48
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
49
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
50
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
51
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.14095.14095.2 4.8369 0.5277 1378.6663 1379.5707 9283.7 1 2692.6 90.9 56 K.MLLESEAFDPAR.S
|
|
52
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.13949.13949.1 2.4766 0.354 1380.67 1379.5707 4485.8 1 506.7 68.2 4 K.MLLESEAFDPAR.S
|
|
53
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_04.14749.14749.2 3.3302 0.2608 1777.8914 1779.0209 3944.1 8 231.6 46.7 9 K.MLLESEAFDPARSGVR.G
|
|
54
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
55
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
56
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
57
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
58
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
59
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
60
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
61
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
62
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
63
|
+
eDeep20120820:eD1_1639_1 6 47 54.6% 97 10181 9.2 U chaperonin GroEL # pI:9.22 MW:10181
|
|
64
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_07.14607.14607.2 3.3369 0.4724 1576.8171 1577.8976 6120.3 1 1543.2 82.1 3 K.MANLGAQMVKEVASK.T
|
|
65
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25402.25402.3 6.2951 0.4542 2466.2097 2467.6519 9066.5 1 4083.4 49 12 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
66
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25380.25380.2 5.5921 0.5669 2466.2104 2467.6519 7538.4 1 2687 64.6 4 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
67
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_02.08539.08539.2 3.2291 0.3305 1215.6385 1216.4381 4640.6 1 1013.9 77.3 4 R.LVAAGSNPMDIK.R
|
|
68
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_07.07029.07029.2 3.8934 0.3124 1371.7393 1372.6256 5850.5 1 1132.1 83.3 23 R.LVAAGSNPMDIKR.G
|
|
69
|
+
eDeep20120820:eD1_1639_1_merge 6 47 54.6% 97 10181 9.2 U chaperonin GroEL # pI:9.22 MW:10181
|
|
70
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.24627.24627.3 3.69 0.2962 2983.4954 2982.231 9369.6 1 1286.9 28.4 1 K.EVASKTSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
71
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25402.25402.3 6.2951 0.4542 2466.2097 2467.6519 9066.5 1 4083.4 49 12 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
72
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25380.25380.2 5.5921 0.5669 2466.2104 2467.6519 7538.4 1 2687 64.6 4 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
73
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_02.08539.08539.2 3.2291 0.3305 1215.6385 1216.4381 4640.6 1 1013.9 77.3 4 R.LVAAGSNPMDIK.R
|
|
74
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_07.07029.07029.2 3.8934 0.3124 1371.7393 1372.6256 5850.5 1 1132.1 83.3 23 R.LVAAGSNPMDIKR.G
|
|
75
|
+
Proteins Peptide IDs Copies
|
|
76
|
+
Unfiltered 93036 400116 424912
|
|
77
|
+
Redundant 390 1292 6998
|
|
78
|
+
Nonredundant 371 1094 5575
|
|
79
|
+
|
|
80
|
+
Classification Nonredundant Proteins Redundant Proteins
|
|
81
|
+
Unclassified 0 0
|
|
@@ -0,0 +1,87 @@
|
|
|
1
|
+
DTASelect v1.9
|
|
2
|
+
/auto/gtl/ms/Abisko_Soils/Field_Sampling_Aug_2010/SurfDeep/Erio_Deep_Aug2010_27Jun_TR1/Frac1/analysis/tryp_edeep_20120820_Mstor4.3.2/sequest
|
|
3
|
+
/auto/gtl/db/Abisko_Soils/edeep_20120820_Mstor4.3.2_cntm_psm
|
|
4
|
+
SEQUEST v.27 in SQT format.
|
|
5
|
+
--DB -p 2 -r 1000
|
|
6
|
+
true Use criteria
|
|
7
|
+
1.8 Minimum +1 XCorr
|
|
8
|
+
2.5 Minimum +2 XCorr
|
|
9
|
+
3.5 Minimum +3 XCorr
|
|
10
|
+
0.08 Minimum DeltCN
|
|
11
|
+
1 Minimum charge state
|
|
12
|
+
3 Maximum charge state
|
|
13
|
+
0 Minimum ion proportion
|
|
14
|
+
1000 Maximum Sp rank
|
|
15
|
+
-1 Minimum Sp score
|
|
16
|
+
Include Modified peptide inclusion
|
|
17
|
+
Any Tryptic status requirement
|
|
18
|
+
true Multiple, ambiguous IDs allowed
|
|
19
|
+
Ignore Peptide validation handling
|
|
20
|
+
XCorr Purge duplicate peptides by protein
|
|
21
|
+
false Include only loci with unique peptide
|
|
22
|
+
false Remove subset proteins
|
|
23
|
+
Ignore Locus validation handling
|
|
24
|
+
0 Minimum modified peptides per locus
|
|
25
|
+
1000 Minimum redundancy for low coverage loci
|
|
26
|
+
2 Minimum peptides per locus
|
|
27
|
+
|
|
28
|
+
Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name
|
|
29
|
+
Unique FileName XCorr DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence
|
|
30
|
+
Mstor_v4.3.2:1344 15 188 58.6% 249 27617 8.7 U Methanoflorens_stordalmirensis_v4.3.2_01361 Methyl-coenzyme M reductase I subunit gamma
|
|
31
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
32
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
33
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05321.05321.1 1.8605 0.2699 822.3913 822.9573 3293.9 1 262 75 2 R.SWMAATR.F
|
|
34
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
35
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
36
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15208.15208.2 4.339 0.4065 1384.6218 1385.5929 6844.7 1 2135.8 90.9 35 K.MLLESEAFDCAR.S
|
|
37
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
38
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
39
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
40
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
41
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
42
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
43
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
44
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
45
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
46
|
+
eDeep20120820:eD1_8237_2 16 220 57.4% 249 27683 8.9 U methyl-coenzyme M reductase gamma subunit # pI:8.94 MW:27683
|
|
47
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.15707.15707.2 3.5762 0.446 1510.7458 1511.6317 5362.4 1 1603.6 80.8 3 R.DVSDDDVVAILGHR.T
|
|
48
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.25883.25883.2 3.5106 0.4492 2228.0544 2229.6162 7158.3 1 1635 70.6 7 R.YIQFTDSMYFAPMVPYVR.S
|
|
49
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08549.08549.2 2.9469 0.2237 1261.665 1262.4111 2571.6 46 401.4 72.7 11 R.FRGVDPGTLSGR.Q
|
|
50
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_11.08730.08730.1 2.0886 0.0945 1261.67 1262.4111 3742.9 146 186.7 50 1 R.FRGVDPGTLSGR.Q
|
|
51
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.14095.14095.2 4.8369 0.5277 1378.6663 1379.5707 9283.7 1 2692.6 90.9 56 K.MLLESEAFDPAR.S
|
|
52
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.13949.13949.1 2.4766 0.354 1380.67 1379.5707 4485.8 1 506.7 68.2 4 K.MLLESEAFDPAR.S
|
|
53
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_04.14749.14749.2 3.3302 0.2608 1777.8914 1779.0209 3944.1 8 231.6 46.7 9 K.MLLESEAFDPARSGVR.G
|
|
54
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.19243.19243.2 4.2447 0.3674 1598.7095 1599.8782 7245.7 1 2066.9 87.5 33 R.LDQNGMMFDMLQR.S
|
|
55
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_01.07956.07956.2 2.6958 0.2148 1332.6833 1333.5426 3808.3 16 374.6 58.3 1 R.SVMNPDGSVSIVK.D
|
|
56
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_06.14773.14773.2 3.112 0.3203 2342.1726 2342.6726 5764 1 382.6 42.9 1 R.SVMNPDGSVSIVKDQVGRPLDK.A
|
|
57
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_05.05981.05981.2 2.9718 0.2878 1427.757 1428.6868 3080.4 18 181.1 50 9 K.AVPVGKPMSDADLK.S
|
|
58
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_10.08906.08906.2 3.2632 0.4873 1670.892 1671.9525 4077.5 1 424.4 60 29 K.AVPVGKPMSDADLKSR.T
|
|
59
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_04.05034.05034.2 2.8362 0.2929 1351.6948 1352.4899 5816.8 2 726.7 68.2 2 R.TTIYRVDGEAAR.A
|
|
60
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_03.09554.09554.2 2.9228 0.3238 1348.7126 1350.5577 7089.2 1 1274.9 80 4 R.ADKELITYIQR.I
|
|
61
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15826.15826.1 2.845 0.4043 1068.4993 1069.3247 6481.2 1 666.4 68.8 21 R.TMWGFKPMA.-
|
|
62
|
+
20120806_Erio_Deep_Aug2010_27Jun_TR1_09.15823.15823.2 3.0173 0.4838 1068.5002 1069.3247 3787.7 1 611.6 81.2 29 R.TMWGFKPMA.-
|
|
63
|
+
eDeep20120820:eD1_1639_1 6 47 54.6% 97 10181 9.2 U chaperonin GroEL # pI:9.22 MW:10181
|
|
64
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_07.14607.14607.2 3.3369 0.4724 1576.8171 1577.8976 6120.3 1 1543.2 82.1 3 K.MANLGAQMVKEVASK.T
|
|
65
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.24627.24627.3 3.69 0.2962 2983.4954 2982.231 9369.6 1 1286.9 28.4 1 K.EVASKTSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
66
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25402.25402.3 6.2951 0.4542 2466.2097 2467.6519 9066.5 1 4083.4 49 12 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
67
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_01.25380.25380.2 5.5921 0.5669 2466.2104 2467.6519 7538.4 1 2687 64.6 4 K.TSDVAGDGTTTATVLAQAIFNEGAR.L
|
|
68
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_02.08539.08539.2 3.2291 0.3305 1215.6385 1216.4381 4640.6 1 1013.9 77.3 4 R.LVAAGSNPMDIK.R
|
|
69
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_07.07029.07029.2 3.8934 0.3124 1371.7393 1372.6256 5850.5 1 1132.1 83.3 23 R.LVAAGSNPMDIKR.G
|
|
70
|
+
CNTM:cont_gi|136429|sp|P00761|TRYP_PIG 10 210 44.6% 231 24409 7.2 U Trypsin precursor # pI:7.00 MW:24410
|
|
71
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_03.15788.15788.2 6.3802 0.5172 2211.1033 2212.424 9002.7 1 3192.2 73.7 43 R.LGEHNIDVLEGNEQFINAAK.I
|
|
72
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_03.15785.15785.3 5.4827 0.3178 2211.104 2212.424 10085.5 1 3737.6 52.6 55 R.LGEHNIDVLEGNEQFINAAK.I
|
|
73
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_09.20588.20588.2 4.8449 0.5284 2283.179 2284.6355 6939.1 1 1631.2 68.4 34 K.IITHPNFNGNTLDNDIMLIK.L
|
|
74
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_09.20736.20736.3 4.4596 0.44 2283.1816 2284.6355 6362.4 1 1148.3 42.1 20 K.IITHPNFNGNTLDNDIMLIK.L
|
|
75
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_05.04620.04620.2 2.6144 0.1022 1044.6127 1046.1686 4628.1 8 508.9 77.8 3 K.LSSPATLNSR.V
|
|
76
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_04.04664.04664.1 2.0106 0.2221 1045.5754 1046.1686 3026.9 18 94.7 50.0 1 K.LSSPATLNSR.V
|
|
77
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_02.16990.16990.2 5.4854 0.5196 1768.7935 1769.985 8295.1 1 2033.6 73.5 48 R.SCAAAGTECLISGWGNTK.S
|
|
78
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_02.17030.17030.3 4.1712 0.2918 1768.7979 1769.985 6647.8 1 1714.8 50.0 3 R.SCAAAGTECLISGWGNTK.S
|
|
79
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_03.19619.19619.2 2.6002 0.3195 1469.7275 1470.6807 3790.9 1 442.0 57.7 1 K.SSGSSYPSLLQCLK.A
|
|
80
|
+
* 20120806_Erio_Deep_Aug2010_27Jun_TR1_04.24767.24767.2 3.1648 0.3948 2158.0327 2159.48 4872.7 1 642.6 55.0 2 K.SSYPGQITGNMICVGFLEGGK.D
|
|
81
|
+
Proteins Peptide IDs Copies
|
|
82
|
+
Unfiltered 93036 400116 424912
|
|
83
|
+
Redundant 390 1292 6998
|
|
84
|
+
Nonredundant 371 1094 5575
|
|
85
|
+
|
|
86
|
+
Classification Nonredundant Proteins Redundant Proteins
|
|
87
|
+
Unclassified 0 0
|