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 make available spectral libraries that are designed to aid in SWATH™ data processing for several species. It enable the ability to query and explore a set of seed datasets from ISB and ETH Zurich followed by on-line, custom analysis of SWATH™ datasets in the repository. User has the option to analyze and repair spectral ion libraries using the DIALib-QC tool.

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

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