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Updated: Jun 13, 2026

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
Published on: August 19, 2025
Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets
Kang Ning1, Damian Fermin, Alexey I Nesvizhskii
1Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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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