Computational analysis of unassigned high‐quality MS/MS spectra in proteomic data sets |
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| Authors: | Kang Ning Damian Fermin Alexey I Nesvizhskii |
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| Institution: | 1. Department of Pathology, University of Michigan, Ann Arbor, MI, USA;2. Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA |
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| Abstract: | In a typical shotgun proteomics experiment, a significant number of high‐quality MS/MS spectra remain “unassigned.” The main focus of this work is to improve our understanding of various sources of unassigned high‐quality spectra. To achieve this, we designed an iterative computational approach for more efficient interrogation of MS/MS data. The method involves multiple stages of database searching with different search parameters, spectral library searching, blind searching for modified peptides, and genomic database searching. The method is applied to a large publicly available shotgun proteomic data set. |
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| Keywords: | Bioinformatics Interactive database search Novel peptides Peptide polymorphisms Spectral quality assessment Unassigned spectra |
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