0587857 - MBÚ 2025 RIV US eng J - Journal Article
Zákopčaník, Marek - Kavan, Daniel - Kukačka, Zdeněk - Novák, Petr - Loginov, Dmitry Sergej
Data-Independent Acquisition Represents a Promising Alternative for Fast Photochemical Oxidation of Proteins (FPOP) Samples Analysis.
Analytical Chemistry. Roč. 96, č. 28 (2024), s. 11273-11279. ISSN 0003-2700. E-ISSN 1520-6882
R&D Projects: GA ČR(CZ) GA22-27695S; GA MŠMT(CZ) EH22_008/0004624; GA TA ČR(CZ) TH86010001
Institutional support: RVO:61388971
Keywords : peptide identification * mass * Oxidation of Proteins
OECD category: Microbiology
Impact factor: 6.8, year: 2023 ; AIS: 1.224, rok: 2023
Method of publishing: Open access
Result website:
https://pubs.acs.org/doi/epdf/10.1021/acs.analchem.4c01084

DOI: https://doi.org/10.1021/acs.analchem.4c01084

Fast Photochemical Oxidation of Proteins (FPOP) is a protein footprinting method utilizing hydroxyl radicals to provide valuable information on the solvent-accessible surface area. The extensive number of oxidative modifications that are created by FPOP is both advantageous, leading to great spatial resolution, and challenging, increasing the complexity of data processing. The precise localization of the modification together with the appropriate reproducibility is crucial to obtain relevant structural information. In this paper, we propose a novel approach combining validated spectral libraries together with utilizing DIA data. First, the DDA data searched by FragPipe are subsequently validated using Skyline software to form a spectral library. This library is then matched against the DIA data to filter out nonrepresentative IDs. In comparison with FPOP data processing using only a search engine followed by generally applied filtration steps, the manually validated spectral library offers higher confidence in identifications and increased spatial resolution. Furthermore, the reproducibility of quantification was compared for DIA, DDA, and MS-only acquisition modes on timsTOF SCP. Comparison of coefficients of variation (CV) showed that the DIA and MS acquisition modes exhibit significantly better reproducibility in quantification (CV medians 0.1233 and 0.1494, respectively) compared to the DDA mode (CV median 0.2104).
Permanent Link: https://hdl.handle.net/11104/0355156


Research data: ProteomeXchange Consortium