Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results

• Published in: Advances in experimental medicine and biology Vol. 919; p. 227
• Main Authors: Lereim, Ragnhild R, Oveland, Eystein, Berven, Frode S, Vaudel, Marc, Barsnes, Harald
• Format: Journal Article
• Language: English
• Published: United States 2016
• Subjects: Algorithms; Animals; Computational Biology - methods; Data Mining - methods; Databases, Protein; High-Throughput Screening Assays; Humans; Proteins - analysis; Proteome; Proteomics - methods; Reproducibility of Results; Search Engine; Software; User-Computer Interface; Workflow; Validation; Protein identification; Visualization; Protein annotation
• DOI: 10.1007/978-3-319-41448-5_11
• ISSN: 0065-2598

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.