Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data DOI Creative Commons
David Teschner, David Gomez‐Zepeda, Mateusz Krzysztof Łącki

и другие.

Journal of Proteome Research, Год журнала: 2025, Номер unknown

Опубликована: Апрель 22, 2025

Mass spectrometry is essential for analyzing and quantifying biological samples. The timsTOF platform a prominent commercial tool this purpose, particularly in bottom-up acquisition scenarios. additional ion mobility dimension requires more complex data processing, yet most current software solutions raw are proprietary or closed-source, limiting integration into custom workflows. We introduce rustims, framework implementing flexible toolbox designed processing data, currently focusing on data-dependent (DDA-PASEF). employs dual-language approach, combining efficient, multithreaded Rust code with an easy-to-use Python interface. This allows implementations that fast, intuitive, easy to integrate. With imspy as its main scripting interface sagepy Sage search engine bindings, rustims enables integrable, intuitive processing. demonstrate capabilities pipeline DDA-PASEF including rescoring of third-party tools like the Prosit intensity predictor extended model. supports tryptic proteomics nontryptic immunopeptidomics benchmark comparisons FragPipe PEAKS. Rustims available GitHub under MIT license, installation packages multiple platforms PyPi all analysis scripts accessible via Zenodo.

Язык: Английский

Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring DOI Creative Commons
Patrick J. Willems, Fabien Théry, Laura Van Moortel

и другие.

Journal of Proteome Research, Год журнала: 2025, Номер unknown

Опубликована: Март 13, 2025

Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted antigens that can serve as vaccine candidates. However, reliable identification epitopes is challenged their extremely low abundance. Here, we describe an optimized bioinformatic framework to enhance the confident immunopeptides. Immunopeptidomics data cell cultures with Listeria monocytogenes were searched four different search engines, PEAKS, Comet, Sage and MSFragger, followed data-driven rescoring MS2Rescore. Compared individual engine results, this integrated workflow boosted immunopeptide average 27% led high-confidence detection 18 additional peptides (+27%) matching 15 proteins (+36%). Despite strong agreement between a small number spectra (<1%) had ambiguous matches multiple excluded ensure identifications. Finally, demonstrate our sensitive timsTOF SCP acquisition find rescoring, now inclusion ion mobility features, identifies 76% more compared Q Exactive HF acquisition. Together, results how integration along maximizes identification, boosting for development.

Язык: Английский

Процитировано

0

Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data DOI Creative Commons
David Teschner, David Gomez‐Zepeda, Mateusz Krzysztof Łącki

и другие.

Journal of Proteome Research, Год журнала: 2025, Номер unknown

Опубликована: Апрель 22, 2025

Mass spectrometry is essential for analyzing and quantifying biological samples. The timsTOF platform a prominent commercial tool this purpose, particularly in bottom-up acquisition scenarios. additional ion mobility dimension requires more complex data processing, yet most current software solutions raw are proprietary or closed-source, limiting integration into custom workflows. We introduce rustims, framework implementing flexible toolbox designed processing data, currently focusing on data-dependent (DDA-PASEF). employs dual-language approach, combining efficient, multithreaded Rust code with an easy-to-use Python interface. This allows implementations that fast, intuitive, easy to integrate. With imspy as its main scripting interface sagepy Sage search engine bindings, rustims enables integrable, intuitive processing. demonstrate capabilities pipeline DDA-PASEF including rescoring of third-party tools like the Prosit intensity predictor extended model. supports tryptic proteomics nontryptic immunopeptidomics benchmark comparisons FragPipe PEAKS. Rustims available GitHub under MIT license, installation packages multiple platforms PyPi all analysis scripts accessible via Zenodo.

Язык: Английский

Процитировано

0