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Langella O, Renne T, Balliau T, Davanture M, Brehmer S, Zivy M, Blein-Nicolas M, Rusconi F. Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. J Proteome Res 2024; 23:3353-3366. [PMID: 39016325 DOI: 10.1021/acs.jproteome.3c00732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Ion mobility mass spectrometry has become popular in proteomics lately, in particular because the Bruker timsTOF instruments have found significant adoption in proteomics facilities. The Bruker's implementation of the ion mobility dimension generates massive amounts of mass spectrometric data that require carefully designed software both to extract meaningful information and to perform processing tasks at reasonable speed. In a historical move, the Bruker company decided to harness the skills of the scientific software development community by releasing to the public the timsTOF data file format specification. As a proteomics facility that has been developing Free Open Source Software (FOSS) solutions since decades, we took advantage of this opportunity to implement the very first FOSS proteomics complete solution to natively read the timsTOF data, low-level process them, and explore them in an integrated quantitative proteomics software environment. We dubbed our software i2MassChroQ because it implements a (peptide)identification-(protein)inference-mass-chromatogram-quantification processing workflow. The software benchmarking results reported in this paper show that i2MassChroQ performed better than competing software on two critical characteristics: (1) feature extraction capability and (2) protein quantitative dynamic range. Altogether, i2MassChroQ yielded better quantified protein numbers, both in a technical replicate MS runs setting and in a differential protein abundance analysis setting.
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Affiliation(s)
- Olivier Langella
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Thomas Renne
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Thierry Balliau
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Marlène Davanture
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Sven Brehmer
- Bruker Software Development, Bruker Daltonics GmbH & Co. KG, Bremen D-28359, Germany
| | - Michel Zivy
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Mélisande Blein-Nicolas
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Filippo Rusconi
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
- INSERM, UMR-S 1138, Centre de Recherche des Cordeliers, Paris F-75005, France
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Veenstra T. Current Methods for Mass Spectrometric Analysis of Intact Proteins and Peptides. Curr Protein Pept Sci 2021; 22:90-91. [PMID: 33998987 DOI: 10.2174/138920372202210308153805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Timothy Veenstra
- School of Pharmacy Cedarville University Cedarville, OH 45314, United States
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