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Methods Mol Biol. 2017;1549:67-74.

Unassigned MS/MS Spectra: Who Am I?

Author information

1
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
2
Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
3
Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia. S.Mathivanan@latrobe.edu.au.

Abstract

Recent advances in high resolution tandem mass spectrometry (MS) has resulted in the accumulation of high quality data. Paralleled with these advances in instrumentation, bioinformatics software have been developed to analyze such quality datasets. In spite of these advances, data analysis in mass spectrometry still remains critical for protein identification. In addition, the complexity of the generated MS/MS spectra, unpredictable nature of peptide fragmentation, sequence annotation errors, and posttranslational modifications has impeded the protein identification process. In a typical MS data analysis, about 60 % of the MS/MS spectra remains unassigned. While some of these could attribute to the low quality of the MS/MS spectra, a proportion can be classified as high quality. Further analysis may reveal how much of the unassigned MS spectra attribute to search space, sequence annotation errors, mutations, and/or posttranslational modifications. In this chapter, the tools used to identify proteins and ways to assign unassigned tandem MS spectra are discussed.

KEYWORDS:

Mass spectrometry; Peptide; Proteins; Proteomics; Unassigned MS/MS spectra

PMID:
27975284
DOI:
10.1007/978-1-4939-6740-7_6
[Indexed for MEDLINE]

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