PT  - JOURNAL ARTICLE
AU  - Hannes L. Röst
AU  - Ruedi Aebersold
AU  - Olga T. Schubert
TI  - Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms
AID  - 10.1101/044552
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 044552
4099  - http://biorxiv.org/content/early/2016/03/18/044552.short
4100  - http://biorxiv.org/content/early/2016/03/18/044552.full
AB  - 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.