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Automated swath data analysis using targeted extraction of ion chromatograms
- Source :
- Proteomics. Methods in Molecular Biology, Methods in Molecular Biology ISBN: 9781493967452, Proteomics: Methods and Protocols, Methods in Molecular Biology, Methods in Molecular Biology-Proteomics
- Publication Year :
- 2017
- Publisher :
- Humana Press, 2017.
-
Abstract
- Targeted mass spectrometry comprises a set of methods able to quantify protein analytes in complex mixtures with high accuracy and sensitivity. These methods, e.g., Selected Reaction Monitoring (SRM) and SWATH MS, use specific mass spectrometric coordinates (assays) for reproducible detection and quantification of proteins. In this protocol, we describe how to analyze, in a targeted manner, data from a SWATH MS experiment aimed at monitoring thousands of proteins reproducibly over many samples. We present a standard SWATH MS analysis workflow, including manual data analysis for quality control (based on Skyline) as well as automated data analysis with appropriate control of error rates (based on the OpenSWATH workflow). We also discuss considerations to ensure maximal coverage, reproducibility, and quantitative accuracy.
- Subjects :
- 0301 basic medicine
Protocol (science)
Swath ms
Analyte
Reproducibility
Computer science
business.industry
Selected reaction monitoring
Pattern recognition
3. Good health
03 medical and health sciences
030104 developmental biology
Targeted mass spectrometry
Data-independent acquisition
Artificial intelligence
business
Targeted proteomics
SWATH
SWATH MS
SWATH acquisition
DIA
OpenSWATH
pyProphet
TRIC aligner
Skyline
Subjects
Details
- Language :
- English
- ISBN :
- 978-1-4939-6745-2
978-1-4939-6747-6 - ISSN :
- 10643745 and 19406029
- ISBNs :
- 9781493967452 and 9781493967476
- Database :
- OpenAIRE
- Journal :
- Proteomics. Methods in Molecular Biology, Methods in Molecular Biology ISBN: 9781493967452, Proteomics: Methods and Protocols, Methods in Molecular Biology, Methods in Molecular Biology-Proteomics
- Accession number :
- edsair.doi.dedup.....b77bfa9716db4a25466e09269bb19159