Characterization of Proteoforms with Unknown Post-translational Modifications Using the MIScore

Journal Article · Fri Aug 05 04:00:00 EDT 2016 · Journal of Proteome Research

DOI:https://doi.org/10.1021/acs.jproteome.5b01098· OSTI ID:1324898

Kou, Qiang; Zhu, Binhai; Wu, Si; Ansong, Charles; Tolić, Nikola; Paša-Tolić, Ljiljana; Liu, Xiaowen

Various proteoforms may be generated from a single gene due to primary structure alterations (PSAs) such as genetic variations, alternative splicing, and post-translational modifications (PTMs). Top-down mass spectrometry is capable of analyzing intact proteins and identifying patterns of multiple PSAs, making it the method of choice for studying complex proteoforms. In top-down proteomics, proteoform identification is often performed by searching tandem mass spectra against a protein sequence database that contains only one reference protein sequence for each gene or transcript variant in a proteome. Because of the incompleteness of the protein database, an identified proteoform may contain unknown PSAs compared with the reference sequence. Proteoform characterization is to identify and localize PSAs in a proteoform. Although many software tools have been proposed for proteoform identification by top-down mass spectrometry, the characterization of proteoforms in identified proteoform-spectrum matches still relies mainly on manual annotation. We propose to use the Modification Identification Score (MIScore), which is based on Bayesian models, to automatically identify and localize PTMs in proteoforms. Experiments showed that the MIScore is accurate in identifying and localizing one or two modifications.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1324898
• Report Number(s): PNNL-SA-119698; 47441; 49209; KP1704020
• Journal Information: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 8 Vol. 15; ISSN 1535-3893
• Publisher: American Chemical Society (ACS)
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Environmental Molecular Sciences Laboratory
post-translational modification
proteoform