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Human Pan-Human library 12,046 proteins
Comprehensive human SWATH library
Rosenberger, G. et al., 2014 (PXD000954)
Proteome coverage 60% (12,046 of 20,218 proteins)
Publication: A repository of assays to quantify 10,000 human proteins by SWATH-MS (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
phl004_canonical_s32_osw.csv SAL00023 TripleTOF OpenSWATH 221.5 MB Download  Customize
phl004_canonical_s32_osw.TraML SAL00025 TripleTOF TraML 1.1 GB Download  
phl004_canonical_s32_osw.txt.QC.tsv SAL00264 TripleTOF Report 3.7 KB Download  
phl004_canonical_s32_osw_decoys.csv SAL00024 TripleTOF OpenSWATH 463.6 MB Download  Customize
phl004_canonical_s32_osw_decoys.TraML SAL00026 TripleTOF TraML 2.1 GB Download  
phl004_canonical_s64_osw.csv SAL00027 TripleTOF OpenSWATH 222.1 MB Download  Customize
phl004_canonical_s64_osw.csv.QC.tsv SAL00265 TripleTOF Report 3.7 KB Download  
phl004_canonical_s64_osw.TraML SAL00029 TripleTOF TraML 1.3 GB Download  
phl004_canonical_s64_osw_decoys.csv SAL00028 TripleTOF OpenSWATH 465.1 MB Download  Customize
phl004_canonical_s64_osw_decoys.TraML SAL00030 TripleTOF TraML 2.6 GB Download  
phl004_canonical_sall_osw.csv SAL00031 TripleTOF OpenSWATH 518.7 MB Download  Customize
phl004_canonical_sall_osw.csv.QC.tsv SAL00266 TripleTOF Report 3.7 KB Download  
phl004_canonical_sall_osw.TraML SAL00033 TripleTOF TraML 2.7 GB Download  
phl004_canonical_sall_osw_decoys.csv SAL00032 TripleTOF OpenSWATH 1.1 GB Download  Customize
phl004_canonical_sall_osw_decoys.TraML SAL00034 TripleTOF TraML 5.5 GB Download  
phl004_canonical_sall_pv.csv SAL00035 TripleTOF Peakview 356.3 MB Download  Customize
phl004_canonical_sall_pv.csv.QC.tsv SAL00267 TripleTOF Report 3.7 KB Download  
phl004_consensus.sptxt SAL00016 TripleTOF Speclib 861.9 MB Download  
phl004_consensus_openms24.TraML SAL00143 TripleTOF TraML 14.2 GB Download  
phl004_consensus_proteotypic_openms24.TraML SAL00144 TripleTOF TraML 13.4 GB Download  


S cerevisiae synthetic peptide full proteome 2013
Yeast SWATH library derived from the Yeast SRM Atlas synthetic peptide data
Picotti et al 2013
Proteome coverage 98%, 6475 of 6607 proteins
Publication: A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
qtrap_final_no_pyroGlu.sptxt SAL00040 QTrap4000 Speclib 172.7 MB Download  
Yeast_QTrap_openswath.tsv SAL00042 QTrap4000 OpenSWATH 17.5 MB Download  Customize
Yeast_QTrap_openswath.tsv.QC.tsv SAL00262 QTrap4000 Report 3.6 KB Download  
Yeast_QTrap_peakview.tsv SAL00041 QTrap4000 Peakview 13.3 MB Download  Customize
Yeast_QTrap_peakview.tsv.QC.tsv SAL00263 QTrap4000 Report 3.6 KB Download  


Human HLA subtypes 5,616 proteins
Human HLA subtype SWATH libraries
Caron, E. et al., 2015 (PXD001904)
Proteome coverage 28% (5,616 of 20,218 proteins)
Publication: An open-source data and computational resource to analyze digital maps of immunopeptidomes (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
A02_human_TripleTOF.sptxt SAL00045 TripleTOF Speclib 9.7 MB Download  
A02_human_TripleTOF_decoy.TraML SAL00043 TripleTOF TraML 28.1 MB Download  
A02_human_TripleTOF_openswath.csv SAL00044 TripleTOF OpenSWATH 2.1 MB Download  Customize
A02_human_TripleTOF_openswath.csv.QC.tsv SAL00250 TripleTOF Report 3.6 KB Download  
A03_human_TripleTOF.sptxt SAL00048 TripleTOF Speclib 3.0 MB Download  
A03_human_TripleTOF_decoy.TraML SAL00046 TripleTOF TraML 14.4 MB Download  
A03_human_TripleTOF_openswath.csv SAL00047 TripleTOF OpenSWATH 1.1 MB Download  Customize
A03_human_TripleTOF_openswath.csv.QC.tsv SAL00256 TripleTOF Report 3.6 KB Download  
A26_human_TripleTOF.sptxt SAL00051 TripleTOF Speclib 1.7 MB Download  
A26_human_TripleTOF_decoy.TraML SAL00049 TripleTOF TraML 6.5 MB Download  
A26_human_TripleTOF_openswath.csv SAL00050 TripleTOF OpenSWATH 486.1 KB Download  Customize
A26_human_TripleTOF_openswath.csv.QC.tsv SAL00251 TripleTOF Report 3.6 KB Download  
B07_human_TripleTOF.sptxt SAL00054 TripleTOF Speclib 16.7 MB Download  
B07_human_TripleTOF_decoy.TraML SAL00052 TripleTOF TraML 43.9 MB Download  
B07_human_TripleTOF_openswath.csv SAL00053 TripleTOF OpenSWATH 3.3 MB Download  Customize
B07_human_TripleTOF_openswath.csv.QC.tsv SAL00257 TripleTOF Report 3.6 KB Download  
B27_human_TripleTOF.sptxt SAL00077 TripleTOF Speclib 5.1 MB Download  
B27_human_TripleTOF_decoy.TraML SAL00075 TripleTOF TraML 18.5 MB Download  
B27_human_TripleTOF_openswath.csv SAL00076 TripleTOF OpenSWATH 1.4 MB Download  Customize
B27_human_TripleTOF_openswath.csv.QC.tsv SAL00252 TripleTOF Report 3.6 KB Download  
B35_human_TripleTOF.sptxt SAL00057 TripleTOF Speclib 336.6 KB Download  
B35_human_TripleTOF_decoy.TraML SAL00055 TripleTOF TraML 1.9 MB Download  
B35_human_TripleTOF_openswath.csv SAL00056 TripleTOF OpenSWATH 137.8 KB Download  Customize
B35_human_TripleTOF_openswath.csv.QC.tsv SAL00258 TripleTOF Report 3.6 KB Download  
B39_human_TripleTOF.sptxt SAL00059 TripleTOF OpenSWATH 11.1 MB Download  Customize
B39_human_TripleTOF_decoy.TraML SAL00060 TripleTOF Speclib 21.9 MB Download  
B39_human_TripleTOF_openswath.csv SAL00058 TripleTOF TraML 1.6 MB Download  
B39_human_TripleTOF_openswath.csv.QC.tsv SAL00253 TripleTOF Report 3.6 KB Download  
B40_human_TripleTOF.sptxt SAL00063 TripleTOF Speclib 13.7 MB Download  
B40_human_TripleTOF_decoy.TraML SAL00061 TripleTOF TraML 29.4 MB Download  
B40_human_TripleTOF_openswath.csv SAL00062 TripleTOF OpenSWATH 2.2 MB Download  Customize
B40_human_TripleTOF_openswath.csv.QC.tsv SAL00259 TripleTOF Report 3.6 KB Download  
B51_human_TripleTOF.sptxt SAL00066 TripleTOF Speclib 1.1 MB Download  
B51_human_TripleTOF_decoy.TraML SAL00064 TripleTOF TraML 4.3 MB Download  
B51_human_TripleTOF_openswath.csv SAL00065 TripleTOF OpenSWATH 317.7 KB Download  Customize
B51_human_TripleTOF_openswath.csv.QC.tsv SAL00254 TripleTOF Report 3.6 KB Download  
B57_human_TripleTOF.sptxt SAL00069 TripleTOF Speclib 1.5 MB Download  
B57_human_TripleTOF_decoy.TraML SAL00067 TripleTOF TraML 5.3 MB Download  
B57_human_TripleTOF_openswath.csv SAL00068 TripleTOF OpenSWATH 404.1 KB Download  Customize
B57_human_TripleTOF_openswath.csv.QC.tsv SAL00260 TripleTOF Report 3.6 KB Download  
C04_human_TripleTOF.sptxt SAL00092 TripleTOF Speclib 1.1 MB Download  
C04_human_TripleTOF_decoy.TraML SAL00090 TripleTOF TraML 3.2 MB Download  
C04_human_TripleTOF_openswath.csv SAL00091 TripleTOF OpenSWATH 243.7 KB Download  Customize
C04_human_TripleTOF_openswath.csv.QC.tsv SAL00255 TripleTOF Report 3.6 KB Download  
DR:DP:DQ_Mtb_ELITE_CID.sptxt SAL00073 Orbitrap Speclib 128.2 MB Download  
DR:DP:DQ_Mtb_ELITE_HCD.sptxt SAL00074 Orbitrap Speclib 88.1 MB Download  
DR:DP:DQ_Mtb_TripleTOF.sptxt SAL00072 TripleTOF Speclib 163.9 MB Download  
DR:DP:DQ_Mtb_TripleTOF_decoy.TraML SAL00070 TripleTOF TraML 374.7 MB Download  
DR:DP:DQ_Mtb_TripleTOF_openswath.csv SAL00071 TripleTOF OpenSWATH 28.6 MB Download  Customize
DR_DP_DQ_Mtb_TripleTOF_openswath.csv.QC.tsv SAL00261 TripleTOF Report 3.7 KB Download  


M. tuberculosis 3,897 proteins
Comprehensive Mycobacterium tuberculosis SWATH library
Schubert, O. et al., 2015 (PASS00656)
Proteome coverage 97% (3,897 of 4,012 proteins)
Publication: Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
Mtb_TubercuList-R27_iRT_UPS_consensus.sptxt SAL00078 TripleTOF Speclib 230.2 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s32_osw.tsv.mz_corrected SAL00286 TripleTOF OpenSWATH 46.7 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s32_osw.tsv.mz_corrected.QC.tsv SAL00290 TripleTOF Report 3.7 KB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s32_osw_decoy.TraML SAL00087 TripleTOF TraML 596.7 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s32_osw_decoy.tsv SAL00081 TripleTOF OpenSWATH 84.0 MB Download  Customize
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s64_osw.tsv.mz_corrected SAL00287 TripleTOF OpenSWATH 48.0 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s64_osw.tsv.mz_corrected.QC.tsv SAL00291 TripleTOF Report 3.7 KB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s64_osw_decoy.TraML SAL00088 TripleTOF TraML 602.7 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_s64_osw_decoy.tsv SAL00083 TripleTOF OpenSWATH 86.8 MB Download  Customize
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_sall_osw.tsv.mz_corrected SAL00288 TripleTOF OpenSWATH 50.1 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_sall_osw.tsv.mz_corrected.QC.tsv SAL00292 TripleTOF Report 3.7 KB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_sall_osw_decoy.TraML SAL00089 TripleTOF TraML 635.0 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_sall_osw_decoy.tsv SAL00085 TripleTOF OpenSWATH 91.1 MB Download  Customize
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_sall_pv.tsv.mz_corrected SAL00289 TripleTOF Peakview 31.1 MB Download  
Mtb_TubercuList-R27_iRT_UPS_noMox_noMC_sall_pv.tsv.mz_corrected.QC.tsv SAL00293 TripleTOF Report 3.7 KB Download  
Mtb_TubercuList-R27_iRT_UPS_raw.sptxt.gz SAL00079 TripleTOF Speclib 820.4 MB Download  


Rat sertoli cells 5,795 proteins
SWATH library from Sertoli cell rat samples from 5 and 12 day animals
Mandal, K. et al., 2017 (PASS00778)
Proteome coverage 27% (5,795 of 21,464 proteins)
Publication: An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
RatSWATHAssayLibrary.sptxt SAL00093 TripleTOF Speclib 87.7 MB Download  
Rattus_norvegicus_cons_peakview_updatedRT_v2.txt.clean SAL00284 TripleTOF Peakview 51.4 MB Download  
Rattus_norvegicus_cons_peakview_updatedRT_v2.txt.clean.QC.tsv SAL00285 TripleTOF Report 3.7 KB Download  


Human SRMAtlas 19,996 proteins
Human SWATH library derived from Human SRM Atlas synthetic peptide QTOF data
Kusebauch, U. et al., 2016
Proteome coverage 99% (19,996 of 20,277 proteins)
Publication: Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
SRMAtlas_2016_openswath.tsv SAL00095 QTOF OpenSWATH 562.2 MB Download  Customize
SRMAtlas_2016_openswath.tsv.QC.tsv SAL00268 QTOF Report 3.7 KB Download  
SRMAtlas_2016_peakview.tsv SAL00096 QTOF Peakview 338.9 MB Download  Customize
SRMAtlas_2016_peakview.tsv.QC.tsv SAL00269 QTOF Report 3.7 KB Download  


M. extorquens PA1 3,489 proteins
Methylobacterium extorquens PA1 - comprehensive library 2016
Müller, D. et al., 2016 (PASS00771)
Proteome coverage 72% (3,489 of 4,829 proteins)
Publication: Systems-level proteomics of two ubiquitous plant commensals reveals complementary adaptive traits for phyllosphere colonization (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
MethylobacteriumExtorquensPA1.tsv.mz_corrected SAL00278 TripleTOF OpenSWATH 55.0 MB Download  
MethylobacteriumExtorquensPA1.tsv.mz_corrected.QC.tsv SAL00279 TripleTOF Reports 3.7 KB Download  
MethylobacteriumExtorquensPA1_consensus.sptxt SAL00116 TripleTOF Speclib 182.4 MB Download  
MethylobacteriumExtorquensPA1_WithDecoys.TraML SAL00099 TripleTOF TraML 613.9 MB Download  


Pseudomonas syringae DC3000 3,580 proteins
Pseudomonas syringae DC3000 - comprehensive library 2016
Müller, D. et al., 2016 (PASS00771)
Proteome coverage 65% (3,580 of 5,481 proteins)
Publication: Systems-level proteomics of two ubiquitous plant commensals reveals complementary adaptive traits for phyllosphere colonization (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
PseudomonasSyringaeDC3000.tsv.mz_corrected SAL00280 TripleTOF OpenSWATH 46.1 MB Download  
PseudomonasSyringaeDC3000.tsv.mz_corrected.QC.tsv SAL00281 TripleTOF Report 3.7 KB Download  
PseudomonasSyringaeDC3000_consensus.sptxt SAL00117 TripleTOF Speclib 154.0 MB Download  
PseudomonasSyringaeDC3000_WithDecoys.TraML SAL00101 TripleTOF TraML 525.0 MB Download  


S. melonis Fr1 2,752 proteins
Sphingomonas melonis Fr1 - comprehensive library 2016
Müller, D. et al., 2016 (PASS00771)
Proteome coverage 71% (2,752 of 3,857 proteins)
Publication: Systems-level proteomics of two ubiquitous plant commensals reveals complementary adaptive traits for phyllosphere colonization (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
SphingomonasMelonisFr1.tsv.mz_corrected SAL00282 TripleTOF OpenSWATH 32.0 MB Download  
SphingomonasMelonisFr1.tsv.mz_corrected.QC.tsv SAL00283 TripleTOF Report 3.7 KB Download  
SphingomonasMelonisFr1_consensus.sptxt SAL00115 TripleTOF Speclib 135.9 MB Download  
SphingomonasMelonisFr1_WithDecoys.TraML SAL00102 TripleTOF TraML 463.0 MB Download  


S. aureus 2,108 proteins
Staphylococcus aureus HG001 SWATH Atlas
Michalik, S. et al., 2017
Proteome coverage 73% (2,108 of 2,891 proteins)
Publication: A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
Saureus_HG001_DIA_library_Michalik_et_al.txt.mz_corrected.QC.tsv SAL00295 TripleTOF Report 3.7 KB Download  
Saureus_HG001_DIA_library_Michalik_et_al.txt.mz_corrected.txt SAL00294 TripleTOF Spectronaut 68.6 MB Download  


Human breast cancer 5,006 proteins
Human Breast Cancer SWATH library
Bouchal, P. et al., 2019 (PASS00857)
Proteome coverage 25% (5,006 of 20,263 proteins)
Publication: Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
BreastCancer_consensus.sptxt SAL00105 TripleTOF Speclib 109.4 MB Download  
BreastCancer_s69_osw.TraML SAL00108 TripleTOF TraML 283.2 MB Download  
BreastCancer_s69_osw.tsv.mz_corrected SAL00272 TripleTOF OpenSWATH 46.0 MB Download  
BreastCancer_s69_osw.tsv.mz_corrected.QC.tsv SAL00274 TripleTOF Report 3.7 KB Download  
BreastCancer_s69_osw_decoy.TraML SAL00106 TripleTOF TraML 568.3 MB Download  
BreastCancer_s69_osw_decoy.tsv SAL00107 TripleTOF OpenSWATH 81.5 MB Download  Customize
BreastCancer_sall_osw.TraML SAL00112 TripleTOF TraML 285.0 MB Download  
BreastCancer_sall_osw.tsv SAL00113 TripleTOF OpenSWATH 48.7 MB Download  Customize
BreastCancer_sall_osw.tsv.QC.tsv SAL00276 TripleTOF Report 3.6 KB Download  
BreastCancer_sall_osw_decoy.TraML SAL00110 TripleTOF TraML 573.6 MB Download  
BreastCancer_sall_osw_decoy.tsv SAL00111 TripleTOF OpenSWATH 83.1 MB Download  Customize
BreastCancer_sall_pvMSH.tsv SAL00273 TripleTOF Peakview 29.7 MB Download  
BreastCancer_sall_pvMSH.txt.QC.tsv SAL00277 TripleTOF Report 3.6 KB Download  


Mouse Immunopeptidome 3,486 proteins
Library of Mouse MHC class I peptides analyzed on TripleTOF (QTOF libs) and Lumos (CID and QTOF-CID libs)
Schuster, H. et al., 2018 (PXD008733)
Proteome coverage 20.5% (3,486 of 16,998 proteins)
Publication: A tissue-based draft map of the murine MHC class I immunopeptidome (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
Db_withMod_iRT_CID-QTOF.sptxt SAL00120 QTOF Speclib 6.4 MB Download  
Db_withMod_iRT_CID-QTOF_osw_correct.QC.tsv SAL00306 QTOF Report 3.6 KB Download  
Db_withMod_iRT_CID-QTOF_osw_correct.tsv SAL00304 QTOF OpenSWATH 3.2 MB Download  
Db_withMod_iRT_CID-QTOF_osw_DECOY.TraML SAL00132 QTOF TraML 39.6 MB Download  
Db_withMod_iRT_CID-QTOF_osw_DECOY.tsv SAL00124 QTOF OpenSWATH 6.7 MB Download  Customize
Db_withMod_iRT_HCD.sptxt SAL00121 Orbitrap Speclib 13.2 MB Download  
Db_withMod_iRT_HCD_osw_correct.QC.tsv SAL00307 QTOF Report 3.6 KB Download  
Db_withMod_iRT_HCD_osw_correct.tsv SAL00305 QTOF OpenSWATH 5.3 MB Download  
Db_withMod_iRT_HCD_osw_DECOY.TraML SAL00133 Orbitrap TraML 66.3 MB Download  
Db_withMod_iRT_HCD_osw_DECOY.tsv SAL00126 Orbitrap OpenSWATH 11.4 MB Download  Customize
Kb_withMod_iRT_CID-QTOF.sptxt SAL00122 QTOF Speclib 5.9 MB Download  
Kb_withMod_iRT_CID-QTOF_osw.QC.tsv SAL00308 QTOF Report 3.6 KB Download  
Kb_withMod_iRT_CID-QTOF_osw.tsv SAL00129 QTOF OpenSWATH 2.6 MB Download  Customize
Kb_withMod_iRT_CID-QTOF_osw_DECOY.TraML SAL00134 QTOF TraML 34.0 MB Download  
Kb_withMod_iRT_CID-QTOF_osw_DECOY.tsv SAL00128 QTOF OpenSWATH 5.6 MB Download  Customize
Kb_withMod_iRT_HCD.sptxt SAL00123 Orbitrap Speclib 11.0 MB Download  
Kb_withMod_iRT_HCD_osw.QC.tsv SAL00309 QTOF Report 3.6 KB Download  
Kb_withMod_iRT_HCD_osw.tsv SAL00131 Orbitrap OpenSWATH 4.1 MB Download  Customize
Kb_withMod_iRT_HCD_osw_DECOY.TraML SAL00135 Orbitrap TraML 52.6 MB Download  
Kb_withMod_iRT_HCD_osw_DECOY.tsv SAL00130 Orbitrap OpenSWATH 8.8 MB Download  Customize


Zebrafish 13,731 proteins
Library generated from 9 different Zebrafish tissues, analyzed with over 100 independent injections
Blattmann, P. et al., 2019 (PASS01237)
Proteome coverage 54% (13,731 of 25,500 proteins)
Publication: Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
SpecLib_cons_LT_102files_64_decoy.TraML SAL00138 TripleTOF TraML 2.2 GB Download  
SpecLib_cons_LT_102files_64_decoy.tsv SAL00137 TripleTOF OpenSWATH 408.5 MB Download  
Zebrafish_consensus_library.sptxt SAL00140 TripleTOF Speclib 795.8 MB Download  
Zebrafish_sall_osw.tsv SAL00141 TripleTOF OpenSWATH 374.0 MB Download  
Zebrafish_sall_osw.tsv.QC.tsv SAL00270 TripleTOF Report 3.7 KB Download  
Zebrafish_sall_osw_decoy.TraML SAL00139 TripleTOF OpenSWATH 4.0 GB Download  
Zebrafish_sall_osw_decoy.tsv SAL00136 TripleTOF OpenSWATH 790.4 MB Download  
Zebrafish_sall_pv.tsv SAL00142 TripleTOF Peakview 262.5 MB Download  
Zebrafish_sall_pv.tsv.QC.tsv SAL00271 TripleTOF Report 3.7 KB Download  


Mouse 10,598 proteins
Comprehensive mouse reference spectral library that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS
Krasny, L. et al., 2020 (PASS01569)
Proteome coverage 62% (10,598 of 16,998 proteins)
Publication: A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
MouseRefSWATH.txt SAL00176 TripleTOF spectronaut 1.1 GB Download  
MouseRefSWATH.txt.QC SAL00179 TripleTOF report 3.6 KB Download  
MouseRefSWATH_iRT.csv SAL00174 TripleTOF spectronaut 1.2 GB Download  
MouseRefSWATH_iRT.txt SAL00173 TripleTOF spectronaut 1.1 GB Download  
MouseRefSWATH_iRT.txt.QC SAL00177 TripleTOF report 3.7 KB Download  
MouseRefSWATH_PeakView.txt SAL00175 TripleTOF Peakview 507.4 MB Download  
MouseRefSWATH_PeakView.txt.QC SAL00178 TripleTOF report 3.7 KB Download  


E. coli 4,087 proteins
An E. coli SWATH assay library from 209 measurements from whole cell lysates grown in different media, over-expressed protein, synthetic peptides and separated by OGE and differential ion mobility samples.
Midha, M. et al., 2020 (PXD020785)
Proteome coverage 93% (4,087 of 4,389 proteins)
Publication: A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
Ecoli_consensus.sptxt SAL00225 TripleTOF speclib 385.4 MB Download  
Ecoli_consensus_openswath.txt SAL00226 TripleTOF OpenSWATH 166.4 MB Download  
Ecoli_consensus_peakview.txt SAL00227 TripleTOF Peakview 96.4 MB Download  
Ecoli_consensus_spectral_library_DQC_reports.txt SAL00222 TripleTOF report 4.4 KB Download  
Ecoli_consensus_T6_100vw_peakview.txt SAL00228 TripleTOF Peakview 48.1 MB Download  
uniprot-proteome_UP000000625_reviewed_yes_crap_DECOY_iRTpeptides.fasta SAL00223 TripleTOF fasta 3.2 MB Download  
uniprot-proteome_UP000000625_reviewed_yes_crap_DECOY_iRTpeptides.ppeps SAL00224 TripleTOF ppeps 3.5 MB Download  


Human T-cell 4,833 proteins
Primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics
Weerakoon, H. et al., 2020 (PASS01587)
Proteome coverage 24% (4,833 of 20,240 proteins)
Publication: A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
Human_Tcell_Consensus_library.pepidx SAL00247 TripleTOF Speclib 1.9 MB Download  
Human_Tcell_Consensus_library.spidx SAL00248 TripleTOF Speclib 417.9 KB Download  
Human_Tcell_Consensus_Library.splib SAL00244 TripleTOF Speclib 150.9 MB Download  
Human_Tcell_Consensus_library.sptxt SAL00245 TripleTOF Speclib 155.5 MB Download  
Human_TCell_OpenSWATH.QC SAL00249 TripleTOF Report 3.6 KB Download  
Human_TCell_OpenSWATH.TraML SAL00243 TripleTOF OpenSWATH 301.8 MB Download  
Human_TCell_OpenSWATH.tsv SAL00241 TripleTOF OpenSWATH 50.7 MB Download  
Human_Tcell_peakview.QC SAL00240 TripleTOF Report 3.6 KB Download  
Human_Tcell_peakview.txt SAL00239 TripleTOF Peakview 34.3 MB Download  
rev_uniprot_Homo_sap_reviewed21112017.fasta SAL00246 TripleTOF Database 25.6 MB Download  


Human DIA Pan-human library 11,848 proteins
A comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples.
Zhu, T. et al., 2020 (PXD015314)
Proteome coverage 56% (11,848 of 20,236 proteins)
Publication: DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery (View)
Hide library files Show library files
Name Accession Instrument Format Size Get Libraries
DPHL1_v1.csv SAL00296 Orbitrap OpenSWATH 491.6 MB Download  
DPHL1_v1.QC.tsv SAL00297 Orbitrap Report 3.6 KB Download  
DPHL1_v1_decoy.csv SAL00298 Orbitrap OpenSWATH 1.0 GB Download  
swissprot_human_20180209_target_IRT_contaminant.fasta SAL00299 Orbitrap fasta 13.2 MB Download  
swissprot_human_20180209_target_IRT_contaminant.ppeps SAL00300 Orbitrap ppeps 13.0 MB Download  


Chinese hamster ovary 13,300 proteins
A comprehensive CHO library, from 63 DDA raw files obtained from the three subcellular organelles, unfractionated (1D) and fractionated CHO-K1 cell lysates.
Sim, K. et al., 2020 (PXD016047)
Proteome coverage 28.5% (13,301 of 46,750 proteins)
Publication: A comprehensive CHO SWATH-MS spectral library for robust quantitative profiling of 10,000 proteins (View)
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Name Accession Instrument Format Size Get Libraries
CHO_appended_with_iRT.fasta SAL00303 TripleTOF fasta 35.4 MB Download  
OneOmics_CHO_Global_Spectral_Library.QC.tsv SAL00302 TripleTOF Report 3.7 KB Download  
OneOmics_CHO_Global_Spectral_Library.txt SAL00301 TripleTOF PeakView 1.2 GB Download  


H. salinarum NRC1 2,578 proteins
Comprehensive DIA/SWATH assay library generated from unfractionated and Off-Gel fractionated H. salinarum NRC-1 lysates grown to mid-exponential and stationary phase, and supplemented with synthetic peptides
Kusebauch U. et. al. 2023 (PXD042770)
Proteome coverage 97% (2,578 proteins of 2,646 proteins)
Publication: A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS (View)
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Name Accession Instrument Format Size Get Libraries
Halobacterium_VNG_cRAP_TargDecoy_plusRT.fasta SAL00314 TripleTOF fasta 1.7 MB Download  
Halobacterium_VNG_cRAP_TargDecoy_plusRT_7-50.ppeps SAL00315 TripleTOF ppeps 1.9 MB Download  
HaloConsLib.sptxt SAL00317 TripleTOF speclib 109.5 MB Download  
HaloTHR49ConsLib.sptxt SAL00316 TripleTOF speclib 44.7 MB Download  
HsalinarumNRC1_VNG_100vw_pv.txt SAL00319 TripleTOF Peakview 46.8 MB Download  
HSalinarumNRC1_VNG_100vw_pv.txt.QC.tsv SAL00313 TripleTOF report 4.3 KB Download  
HsalinarumNRC1_VNG_all_pv.txt SAL00318 TripleTOF Peakview 52.3 MB Download  
HSalinarumNRC1_VNG_all_pv.txt.QC.tsv SAL00312 TripleTOF report 3.7 KB Download  


Human DIA Pan-human library 13,465 proteins
A comprehensive DIA pan-human library, from 1608 data-dependent acquisition (DDA) MS raw files for 24 human tissue types.
Xue Z. et. al. 2023 (PXD039313)
Proteome coverage 66% (13,465 of 20,350 proteins)
Publication: DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins (View)
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Name Accession Instrument Format Size Get Libraries
2020-07-17-decoys-UP000005640_reviewed_human_20200401_irt_fragpipe.fasta SAL00326 Orbitrap fasta 25.7 MB Download  
2020-08-05-decoys-UP000005640_isoform_reviewed_human_20200401_irt_fragpipe.fasta SAL00327 Orbitrap fasta 55.0 MB Download  
DPHL_v2_isoformfull_reviewed.QC.tsv SAL00325 Orbitrap Report 3.7 KB Download  
DPHL_v2_isoformfull_reviewed.tsv SAL00323 Orbitrap Prosit 1.7 GB Download  
DPHL_v2_reviewed.QC.tsv SAL00324 Orbitrap Report 3.7 KB Download  
DPHL_v2_reviewed.tsv SAL00322 Orbitrap Prosit 1.5 GB Download  


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