# i2MassChroQ: Software for Ion Mobility-Enabled Quantitative Proteomics in timsTOF Data Format

Olivier Langella, Thomas Renne, Thierry Balliau, Marlène Davanture, Sven

Brehmer, Michel Zivy, Melisande Blein-Nicolas, Filippo Rusconi

► To cite this version:

Olivier Langella, Thomas Renne, Thierry Balliau, Marlène Davanture, Sven Brehmer, et al. i2MassChroQ: Software for Ion Mobility-Enabled Quantitative Proteomics in timsTOF Data Format. Analytics 2022, Sep 2022, Nantes, France. [hal-03776788](https://hal.science/hal-03776788)

HAL Id: hal-03776788

https://hal.science/hal-03776788

Submitted on 14 Sep 2022

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Distributed under a Creative Commons Attribution 4.0 International License
# i2MassChroQ: Software for Ion Mobility-Enabled Quantitative Proteomics in timsTOF Data Format

Olivier Langella*, Thomas Renne, Thierry Balliau, Marlène Davanture, Sven Brehmer, Michel Zivy, Mélisande Blein-Nicolas and Filippo Rusconi

olivier.langella@universite-paris-saclay.fr - filippo.rusconi@universite-paris-saclay.fr

IDEEV - Institut diversité, écologie et évolution du vivant

GQE-Le Moulon, PAPPSO

Université Paris-Saclay, INRAE, CNRS, AgroParisTech,

F-91190 Gif-sur-Yvette, France

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## ABSTRACT

X!TandemPipeline (Langella et al. 2017) is a free and open source Java software program for proteomics initially designed to filter and group peptide/protein identifications from MS/MS mass spectra. After a complete rewrite in C++17, the new X!TandemPipeline++ program features peptide/protein quantification, in particular with support for native timsTOF raw data.

X!TandemPipeline++ performs peptide identifications and area-under-the-curve XIC-based quantifications using the Bruker's native timsTOF raw data format. Using a common HeLa data set, published by Meier et al. (2018, PXD010012), we demonstrate that X!TandemPipeline++ identifies and quantifies significantly more proteins than the MaxQuant and MSFragger competitors, while being also significantly faster.

Please, note that X!TandemPipeline++ will soon be renamed to i2MassChroQ to reflect the identification & inference — mass chromatogram-based quantification capabilities.

## RESULTS

### Identification and protein inference

X!TandemPipeline++ features high throughput and high resolution proteomics and metaproteomics features.

Thousands of DDA identification results can be loaded at once as part of the same project.

Our software supports Mascot-, X!Tandem-generated identification data or any data set in mzIdentML and pepXML formats (from OpenMS, Comet, PeptideProphet). Its Occam's razor-based grouping algorithm can infer protein groups very quickly, in particular by filtering-out non informative redundancies (Van Den Bossche et al., nature communications, 2021).

Grouping might be performed by processing each sample separately or by creating a consensus protein list starting from multiple combined samples.

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## Quantitative analysis

Peptide quantification is handled by calculating extracted ion current chromatograms from precursor ion MS data (MassChroQ module).

Protein quantification is performed by the MCQR module that computes protein intensities by filtering and aggregating peptide intensities and carrying over cluster analysis, ANOVA, and comparisons between treatments.

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## timsTOF data native support

Our native C++-based timsTOF raw data reader was developed from scratch thanks to the technical specifications provided by Bruker. Tight optimizations were needed to ensure super-fast access to the Bruker-encoded binary data.

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The current version provides real time MS/MS peptide annotation and performs extremely fast ion current extraction and XIC chromatogram visualization.

Conversion speed from TimsTOF format to open standards (mzML or mzXML) is 2 times faster with

our raw data parser compared to msconvert using the Bruker's native DLL.

## TimsTOF PASEF quantification reproducibility

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While quantifying more proteins than competitors (1 ion or more), X!TandemPipeline still shows excellent correlations between replicates and very low median CV (4 Hela technical replicates, PXD10012)

## Quantification accuracy

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Plot of the 6428 proteins quantified (2 ions or more) and compared to ground truth ratio (2:1 for Yeast, 1:1 for Human, 1:4 for Ecoli, PXD01477)

## AVAILABILITY

i2MassChroQ and its user manual are available as Free Software, licensed under the GNU General Public License (v3 +). The user manual is available in PDF or HTML format. i2MassChroQ is developed on Debian GNU/Linux. Binary packages are built for GNU/Linux and MS Windows. GIT repository: https://forgemia.inra.fr/pappso/i2masschroq.

### Main website

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### User manuals

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<footnote>* presenting and corresponding author</footnote>