Cited 2 time in webofscience Cited 2 time in scopus

Statistical Modeling for Enhancing the Discovery Power of Citrullination from Tandem Mass Spectrometry Data

Title
Statistical Modeling for Enhancing the Discovery Power of Citrullination from Tandem Mass Spectrometry Data
Authors
Huh, SunghyunHwang, DaeheeKim, Min-Sik
DGIST Authors
Hwang, Daehee; Kim, Min-Sik
Issue Date
2020-10
Citation
Analytical Chemistry, 92(19), 12975-12986
Type
Article
Article Type
Article
Keywords
NEUTRAL LOSSIDENTIFICATIONFRAGMENTATIONPROTEINSSPECTRAPROBE
ISSN
0003-2700
Abstract
Citrullination is a post-translational modification implicated in various human diseases including rheumatoid arthritis, Alzheimer's disease, multiple sclerosis, and cancers. Due to a relatively low concentration of citrullinated proteins in the total proteome, confident identification of citrullinated proteome is challenging in mass spectrometry (MS)-based proteomic analysis. From these MS-based analyses, MS features that characterize citrullination, such as immonium ions (IMs) and neutral losses (NLs), called diagnostic ions, have been reported. However, there has been a lack of systematic approaches to comprehensively search for diagnostic ions and no statistical methods for the identification of citrullinated proteome based on these diagnostic ions. Here, we present a systematic approach to identify diagnostic IMs, internal ions (INTs), and NLs for citrullination from tandem mass (MS/MS) spectra. Diagnostic INTs mainly consisted of internal fragment ions for di- and tripeptides that contained two and three amino acids with at least one citrullinated arginine, respectively. A statistical logistic regression model was built for a confident assessment of citrullinated peptides that database searches identified (true positives) and prediction of citrullinated peptides that database searches failed to identify (false negatives) using the diagnostic IMs, INTs, and NLs. Applications of our model to complex global proteome data sets demonstrated the increased accuracy in the identification of citrullinated peptides, thereby enhancing the size and functional interpretation of citrullinated proteomes. Copyright © 2020 American Chemical Society.
URI
http://hdl.handle.net/20.500.11750/12669
DOI
10.1021/acs.analchem.0c01687
Publisher
American Chemical Society
Related Researcher
  • Author Kim, Min-Sik Laboratory for QBIO and Precision Medicine
  • Research Interests Cancer Proteogenomics, Biomarker Discovery, Integrative Multi-Omics
Files:
There are no files associated with this item.
Collection:
Department of New BiologySystems Biology and Medicine Lab1. Journal Articles
Department of New BiologyLaboratory for QBIO and Precision Medicine1. Journal Articles


qrcode mendeley

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

BROWSE