title: A novel spectral library workflow to enhance protein identifications.
abstract: The innovations in mass spectrometry-based investigations in proteome biology enable systematic characterization of molecular details in pathophysiological phenotypes. However, the process of delineating large-scale raw proteomic datasets into a biological context requires high-throughput data acquisition and processing. A spectral library search engine makes use of previously annotated experimental spectra as references for subsequent spectral analyses. This workflow delivers many advantages, including elevated analytical efficiency and specificity as well as reduced demands in computational capacity. In this study, we created a spectral matching engine to address challenges commonly associated with a library search workflow. Particularly, an improved sliding dot product algorithm, that is robust to systematic drifts of mass measurement in spectra, is introduced. Furthermore, a noise management protocol distinguishes spectra correlation attributed from noise and peptide fragments. It enables elevated separation between target spectral matches and false matches, thereby suppressing the possibility of propagating inaccurate peptide annotations from library spectra to query spectra. Moreover, preservation of original spectra also accommodates user contributions to further enhance the quality of the library. Collectively, this search engine supports reproducible data analyses using curated references, thereby broadening the accessibility of proteomics resources to biomedical investigators. This article is part of a Special Issue entitled: From protein structures to clinical applications.
authors: Department of Physiology, UCLA School of Medicine, Los Angeles, CA 90095, USA.
authors: Haomin
authors: H
authors: Li
authors: Nobel C
authors: NC
authors: Zong
authors: Xiangbo
authors: X
authors: Liang
authors: Allen K
authors: AK
authors: Kim
authors: Jeong Ho
authors: JH
authors: Choi
authors: Ning
authors: N
authors: Deng
authors: Ivette
authors: I
authors: Zelaya
authors: Maggie
authors: M
authors: Lam
authors: Huilong
authors: H
authors: Duan
authors: Peipei
authors: P
authors: Ping
mesh_terms: D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D019151:Peptide Library
chemical_list: D019151:Peptide Library
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