Chapter 9: Informatics Solutions for Selected Reaction Monitoring

Birgit Schilling, Brendan MacLean, Jason M. Held, Bradford W. Gibson

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Informatics solutions for SRM assays pose several specific bioinformatics challenges including assay development, generating acquisition methods, and data processing. Furthermore, SRM is often coupled to experimental designs using stable isotope dilution SRM mass spectrometry workflows (SID-SRM-MS) that utilize one or more stable isotope versions of the analyte as internal standards. Skyline, an open-source software suite of tools for targeted proteomics, has emerged as the most widely used platform for SRM-specific assays. Skyline is a freely-available, comprehensive tool with high versatility for SRM assay development and subsequent processing of data acquired on triple quadrupole mass spectrometers. Skyline can be used for peptide and transition selection, assay optimization, retention time scheduling, SRM instrument method export, peak detection/integration, post-acquisition signal processing, and integration with statistical tools and algorithms to generate quantitative results for peptides and proteins. To highlight some of the Skyline SRM functionalities, we describe features including important visual displays and statistical tools, including 'External Tools'. We discuss Skyline features that are particularly valuable for system suitability assessments, as well as for data sets with posttranslational modifications. Finally, an easy, point-and-click strategy is presented that supports dissemination of SRM data processed in Skyline to the Panorama web data repositories.

Original languageEnglish
Title of host publicationProteome Informatics
EditorsSimon J. Gaskell, Conrad Bessant
PublisherRoyal Society of Chemistry
Pages178-199
Number of pages22
Edition5
ISBN (Electronic)9781782624288
DOIs
StatePublished - Jan 1 2017

Publication series

NameNew Developments in Mass Spectrometry
Number5
Volume2017-January
ISSN (Electronic)2045-7553

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    Schilling, B., MacLean, B., Held, J. M., & Gibson, B. W. (2017). Chapter 9: Informatics Solutions for Selected Reaction Monitoring. In S. J. Gaskell, & C. Bessant (Eds.), Proteome Informatics (5 ed., pp. 178-199). (New Developments in Mass Spectrometry; Vol. 2017-January, No. 5). Royal Society of Chemistry. https://doi.org/10.1039/9781782626732-00178