Label-free quantitative shotgun proteomics using normalized spectral abundance factors

Karlie A. Neilson, Tim Keighley, Dana Pascovici, Brett Cooke, Paul A. Haynes

Research output: Chapter in Book/Report/Conference proceedingChapter

42 Citations (Scopus)


In this chapter we describe the work fl ow used in our laboratory for label-free quantitative shotgun proteomics based on spectral counting. The main tools used are a series of R modules known collectively as the Scrappy program. We describe how to go from peptide to spectrum matching in a shotgun proteomics experiment using the XTandem algorithm, to simultaneous quanti fi cation of up to thousands of proteins, using normalized spectral abundance factors. The outputs of the software are described in detail, with illustrative examples provided for some of the graphical images generated. While it is not strictly within the scope of this chapter, some consideration is given to how best to extract meaningful biological information from quantitative shotgun proteomics data outputs.

Original languageEnglish
Title of host publicationProteomics for Biomarker Discovery
EditorsMing Zhou, Timothy Veenstra
Place of PublicationNew York
PublisherHumana Press
Number of pages18
ISBN (Electronic)9781627033602
ISBN (Print)9781627033596
Publication statusPublished - 2013

Publication series

NameMethods in Molecular Biology: Methods and Protocols
ISSN (Print)1064-3745

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