Journal Article

DKFZ-2025-00844

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.

Teschner, D. ; Gómez-Zepeda, D.DKFZ* ; Łącki, M. K. ; Kemmer, T. ; Busch, A. ; Tenzer, S.DKFZ* ; Hildebrandt, A.

2025
ACS Publications Washington, DC

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Please use a persistent id in citations: doi:10.1021/acs.jproteome.4c00966

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

Keyword(s): DDA-PASEF ; Python ; framework ; ion mobility ; mass spectrometry ; open-source ; proteomics ; rust-lang ; timsTOF

Note: 2025 May 2;24(5):2358-2368

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Contributing Institute(s):

1. HI-TRON zentral (D190)
2. Hi-TRON Immunoproteomik (D191)

Research Program(s):

1. 314 - Immunologie und Krebs (POF4-314) (POF4-314)

Appears in the scientific report 2025

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Database coverage:
; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; Essential Science Indicators ; IF < 5 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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