Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package
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Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. / Langella, Olivier; Renne, Thomas; Balliau, Thierry; Davanture, Marlène; Brehmer, Sven; Zivy, Michel; Blein-Nicolas, Mélisande; Rusconi, Filippo.
In: J PROTEOME RES, Vol. 23, No. 8, 02.08.2024, p. 3353-3366.Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review
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TY - JOUR
T1 - Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package
AU - Langella, Olivier
AU - Renne, Thomas
AU - Balliau, Thierry
AU - Davanture, Marlène
AU - Brehmer, Sven
AU - Zivy, Michel
AU - Blein-Nicolas, Mélisande
AU - Rusconi, Filippo
PY - 2024/8/2
Y1 - 2024/8/2
N2 - 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.
AB - 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.
U2 - 10.1021/acs.jproteome.3c00732
DO - 10.1021/acs.jproteome.3c00732
M3 - SCORING: Journal article
C2 - 39016325
VL - 23
SP - 3353
EP - 3366
JO - J PROTEOME RES
JF - J PROTEOME RES
SN - 1535-3893
IS - 8
ER -