Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results
Shotgun proteomics is a high throughput technique for protein identification able to identify up to several thousand proteins from a single sample. In order to make sense of this large amount of data, proteomics analysis software is needed, aimed at making the data intuitively accessible to beginners as well as experienced scientists. This chapter provides insight on where to start when analyzing shotgun proteomics data, with a focus on explaining the most common pitfalls in protein identification analysis and how to avoid them. Finally, the move to seeing beyond the list of identified proteins and to putting the results into a bigger biological context is discussed.
KeywordsProtein identification Visualization Protein annotation Validation
Peptide Spectrum Match
False Discovery Rate
False Negative Rate
R.R.L, E.O. and F.S.B. acknowledge the support by Kjell Alme’s Legacy for Research in Multiple Sclerosis, and the Kristian Gerhard Jebsen Foundation. H.B. is supported by the Research Council of Norway.