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OpenSWATH specifications


Unique identifier OMICS_07613
Name OpenSWATH
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Parallelization OpenMP
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline George Rosenberger

Publication for OpenSWATH

OpenSWATH citations


Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

Microb Genom
PMCID: 5885015
PMID: 29557774
DOI: 10.1099/mgen.0.000163
call_split See protocol

[…] ATH mode on a TripleTOF 5600 mass spectrometer using data-independent acquisition settings as described earlier []. Resulting raw SWATH data were analysed using an automated pipeline and the software OpenSWATH with the M. tuberculosis H37Rv SWATH assay library []. Differential expression analysis of proteins identified in M. tuberculosis H37Rv and M. bovis AF2122/97 samples was dependent on the de […]


Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

Cell Syst
PMCID: 5747350
PMID: 29226804
DOI: 10.1016/j.cels.2017.11.002

[…] ured on the iPortal platform in the lab (). The raw SWATH wiff files were converted using ProteoWizard (version 3.0.5533) to profile mzXML files (). The extraction of the data was performed using the OpenSWATH workflow () and the combined human assay library (). An m/z fragment ion extraction window of 0.05 Th, an RT extraction window of 600 s and a set of 10 different scores were used. To match f […]


Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

Nat Commun
PMCID: 5663699
PMID: 29089484
DOI: 10.1038/s41467-017-01422-6

[…] For analyzing the steady-state proteomes of twin samples and unrelated samples, the SWATH-MS identification was performed by OpenSWATH software searching against a previously established SWATH assay library, which contains mass spectrometric assays for 10,000 human proteins. OpenSWATH first identified the peak groups from a […]


Multi laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH mass spectrometry

Nat Commun
PMCID: 5566333
PMID: 28827567
DOI: 10.1038/s41467-017-00249-5
call_split See protocol

[…] acquired at different sites was investigated by comparing the set of inferred proteins detected from the HEK293 proteome across all 229 SWATH-MS data files. Targeted analysis was performed using the OpenSWATH software combined with a previously published SWATH-MS spectral library containing peptide query parameters mapping to 10,000+ human proteins (Fig. ). The false discovery rate (FDR) was cont […]


Statistical control of peptide and protein error rates in large scale targeted DIA analyses

Nat Methods
PMCID: 5581544
PMID: 28825704
DOI: 10.1038/nmeth.4398
call_split See protocol

[…] The analysis of the inter-laboratory SWATH-MS dataset was conducted identically as described previously. The SWATH-MS data analysis was performed using OpenSWATH (OpenMS v2.0) essentially as described with the following modified parameters: m/z extraction window = 75 ppm, RT extraction window = 900 seconds. The analysis was performed separately for t […]


Impact of Alternative Splicing on the Human Proteome

Cell Rep
PMCID: 5554779
PMID: 28768205
DOI: 10.1016/j.celrep.2017.07.025

[…] The accession number for the raw data of mass spectrometry measurements (SWATH-MS and shotgun) together with the input spectral library and OpenSWATH results reported in this paper is ProteomeXchange Consortium ( PXD003278. The accession number for the RNA sequencing data reported in this paper […]


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OpenSWATH institution(s)
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

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