Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F24%3A00585513" target="_blank" >RIV/61388971:_____/24:00585513 - isvavai.cz</a>
Alternative codes found
RIV/61388971:_____/23:00583029 RIV/00216208:11310/23:10473381
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00390" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00390</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jproteome.3c00390" target="_blank" >10.1021/acs.jproteome.3c00390</a>
Alternative languages
Result language
angličtina
Original language name
Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10606 - Microbiology
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2024
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Proteome Research
ISSN
1535-3893
e-ISSN
1535-3907
Volume of the periodical
23
Issue of the periodical within the volume
2
Country of publishing house
US - UNITED STATES
Number of pages
9
Pages from-to
609-617
UT code for WoS article
001157569300001
EID of the result in the Scopus database
2-s2.0-85181560169