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000300630 041__ $$aEnglish
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000300630 1001_ $$00000-0002-1755-5382$$aTeschner, David$$b0
000300630 245__ $$aRustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.
000300630 260__ $$aWashington, DC$$bACS Publications$$c2025
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000300630 500__ $$a2025 May 2;24(5):2358-2368
000300630 520__ $$aMass 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.
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000300630 650_7 $$2Other$$aDDA-PASEF
000300630 650_7 $$2Other$$aPython
000300630 650_7 $$2Other$$aframework
000300630 650_7 $$2Other$$aion mobility
000300630 650_7 $$2Other$$amass spectrometry
000300630 650_7 $$2Other$$aopen-source
000300630 650_7 $$2Other$$aproteomics
000300630 650_7 $$2Other$$arust-lang
000300630 650_7 $$2Other$$atimsTOF
000300630 7001_ $$0P:(DE-He78)4569ef2919d2438765ad71515f53646b$$aGómez-Zepeda, David$$b1$$udkfz
000300630 7001_ $$00000-0001-7415-4748$$aŁącki, Mateusz K$$b2
000300630 7001_ $$00000-0003-1180-746X$$aKemmer, Thomas$$b3
000300630 7001_ $$00009-0002-7955-821X$$aBusch, Anne$$b4
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000300630 7001_ $$aHildebrandt, Andreas$$b6
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