Počet záznamů: 1
Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis
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SYSNO ASEP 0583029 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis Tvůrce(i) Zákopčaník, Marek (MBU-M) ORCID
Kavan, Daniel (MBU-M) RID, ORCID
Novák, Petr (MBU-M) RID, ORCID
Loginov, Dmitry Sergej (MBU-M) RIDZdroj.dok. Journal of Proteome Research. - : American Chemical Society - ISSN 1535-3893
Roč. 23, č. 2 (2023), s. 609-617Poč.str. 9 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova mass-spectrometry ; exchange ; fpop ; searchengine ; structural proteomics Obor OECD Microbiology Způsob publikování Open access Institucionální podpora MBU-M - RVO:61388971 UT WOS 001157569300001 EID SCOPUS 85181560169 DOI 10.1021/acs.jproteome.3c00390 Anotace Fast Photochemical Oxidation of Proteins (FPOP) is a promising technique for studying protein structure and dynamics. The quality of insight provided by FPOP depends on the reliability of the determination of the modification site. This study investigates the performance of two search engines, Mascot and PEAKS, for the data processing of FPOP analyses. Comparison of Mascot and PEAKS of the hemoglobin--haptoglobin Bruker timsTOF data set (PXD021621) revealed greater consistency in the Mascot identification of modified peptides, with around 26% of the IDs being mutual for all three replicates, compared to approximately 22% for PEAKS. The intersection between Mascot and PEAKS results revealed a limited number (31%) of shared modified peptides. Principal Component Analysis (PCA) using the peptide-spectrum match (PSM) score, site probability, and peptide intensity was applied to evaluate the results, and the analyses revealed distinct clusters of modified peptides. Mascot showed the ability to assess confident site determination, even with lower PSM scores. However, high PSM scores from PEAKS did not guarantee a reliable determination of the modification site. Fragmentation coverage of the modification position played a crucial role in Mascot assignments, while the AScore localizations from PEAKS often become ambiguous because the software employs MS/MS merging. Pracoviště Mikrobiologický ústav Kontakt Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Rok sběru 2024 Elektronická adresa https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00390
Počet záznamů: 1