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The SWATHAtlas at the Institute for Systems Biology is a resource for planning your SWATH™ experiments, depositing published SWATH™ experiments, and exploring the results of deposited datasets.

The SWATHAtlas project is still in development. Phase 1 of the project will make available some initial spectral libraries that are designed to aid in SWATH™ data processing for several species. Phase 2 will enable the ability to query and explore a set of seed datasets from ISB and ETH Zurich. Phase 3 will enable on-line, custom analysis of SWATH™ datasets in the repository.



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Current SWATH Libraries

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Library Proteome Coverage Contributors
Ecoli 4,000 protein 2020 ~92% covering 4,014 of the 4,389 annotated E. coli proteins Midha M. et. al.
H sapiens 10,000 protein 2014 51%, 10,316 of 20218 proteins Rosenberger et al 2014
H sapiens HLA subtypes Caron et al 2014
Human SRMAtlas 2016 99% Kusebauch, Moritz et al
Human breast cancer library 2019 Bouchal et al. 2019
HumanTcell2020 24% (4,833 of 20,240 proteins) Weerakoon H. et. al. 2020
M tuberculosis comprehensive library 2015 99%, 3984 of 4012 proteins Schubert et. al 2015
Methylobacterium extorquens PA1 - comprehensive library 2016 71%, 3440 of 4829 proteins Müller et al., 2016
Mouse Immunopeptidome Caron et al 2018
MouseRefSWATH 62.2% (10597 of 16998 proteins) Krasny et. al. 2020
Pseudomonas syringae DC3000 - comprehensive library 2016 62%, 3406 of 5481 proteins Müller et al., 2016
Rat (Sertoli cell) 14.6%, 3127 of 21,464 proteins Dr. Kamal Mandal et. al
S aureus HG001 SWATH Atlas 72% (2091 of 2891 proteins) Michalik S, Schmidt F, et al
S cerevisiae synthetic peptide full proteome 2013 98%, 6475 of 6607 proteins Picotti et al 2013
Sphingomonas melonis Fr1 - comprehensive library 2016 71%, 2729 of 3857 proteins Müller et al., 2016
Zebrafish multi-tissue 2019 40.4%, 10,405 of ~25,500 proteins (ensembl) Blattmann et al


SWATH Atlas News

2020-10-16: DIALib-QC ion-library assessment tool published in Nature Communication.
2020-09-29: HumanTcell2020 released (Weerakoon H et. al 2020).
2020-09-15: Ecoli SWATH assay library released (Midha M et. al 2020).
2020-06-18: Comprehensive mouse reference spectral library (Kransy et. al 2020).
2019-11-08: DIALib-QC ion-library assessment tool released.
2018-05-29: Mouse MHC Class I Immunopeptidome released (Caron et al).
2017-09-07: Staphylococcus aureus HG001 SWATH libraries released (Schmidt et al).
2016-03-06: Human breast cancer SWATH libraries released (Bouchal et al).
2015-07-14: Human HLA immunoproteome SWATH libraries released (Caron et al).
2015-05-04: Comprehensive M tuberculosis SWATH library released (Schubert et al. in press).
2014-08-06: Human 10,000 protein SWATH library released (Rosenberger et al. 2014 (in press)).              
2014-04-08: Dr. Samuel Bader presents SWATH Atlas at US HUPO in Seattle.
2014-04-04: Mtb SWATH libraries based on Mtb SRM Atlas data released (Schubert et al. 2013 ).
2014-04-01: SWATHAtlas.org website launched





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