Full native timsTOF PASEF-enabled quantitative proteomics with the i2MassChroQ software package
Résumé
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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