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Poster De Conférence Année : 2022

X!TandemPipeline++: Software for Ion Mobility-Enabled Quantitative Proteomics in timsTOF Data Format

Résumé

Introduction X!TandemPipeline (Langella et al. 2017) is a proteomics free and open source Java software program designed to filter and group peptide/protein identifications from MS/MS mass spectra. After a complete rewrite in C++17, X!TandemPipeline++ now features both native support for the timsTOF raw data format and peptide/protein quantification. X!TandemPipeline++ performs peptide identifications and area under the curve XIC-based quantifications using the Bruker's native raw data format. Using a common HeLa data set published by Meier et al. (2018, PXDO1OO12), we demonstrate that X!TandemPipeline++ identifies and quantifies significantly more proteins than competitors MaxQuant and MSFragger. It is also significantly faster. Methods X!TandemPipeline++ is written in portable C++17 and makes use of the Qt libraries for the graphical user interface. Binary packages are available for Linux and MS Windows. The timsTOF native raw data reader was developed in-house with the technical specifications provided by Bruker. The sofware was tightly optimized to ensure very fast access to the binary data. The current version provides real time MS/MS peptide annotation and performs extremely fast ion current extractions and XIC chromatogram visualizations (typically, in less than five seconds for a 2 hour PASEF run). Preliminary Data or Plenary Speakers Abstract The Bruker timsTOF line of instruments improves the identification of peptides and proteins in complex mixtures by implementing a peculiar ion mobility technology. X!TandemPipeline++ has the distinct feature, with respect to the MaxQuant and MSFragger competitors, of natively parsing the timsTOF raw data with original software code that puts us in total control of the data processing, in particular where tight optimizations are needed for speed or in cases where special data processing features need adding for increased accuracy. This is exemplified by X!TandemPipeline++ using the renowned X!Tandem engine (Craig et al. 2004) to perform database searches right on optimized data brokered to it by our reader of native timsTOF binary data. Our software identifies roughly the same amount of peptides as when using the X!Tandem engine on MGF data provided by the Bruker Data analysis tool but performs much faster, reducing processing time from 55 to 12 minutes on a typical quality control HeLa sample. For peptide quantifications, X!TandemPipeline++ uses the ion mobility-enabled version of MassChroQ (Valot et al. 2011), both software pieces sharing our optimized native timsTOF data reader. Using a common HeLa data set (Meier et al. (2018), PXDO1OO12, 4 technical replicates), we found more quantified proteins with a minimum of 2 quantified ions : 5783 vs 4977 (MSFragger), 3526 (MaxQuant). Correlation of quantified proteins between samples was 0.99. Median protein coefficient of variation (CV) was also very good : 0.059 vs 0.049 (MSFragger), 0.072 (Peaks) and 0.070 (MaxQuant). Comparable results have been found using data set PXD014777 (Prianichnikov et al., 2020, a mixture of proteins from three organisms, H. sapiens, S. cerevisiae, and E. coli). Overall, while producing similar or better results than competing software, X!TandemPipeline++ always performs faster than all the other software offerings. Novel Aspect Fast and accurate timsTOF native raw data support for quantitative proteomics.
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hal-03687564 , version 1 (03-06-2022)

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  • HAL Id : hal-03687564 , version 1

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Olivier Langella, Thomas Renne, Thierry Balliau, Marlène Davanture, Sven Brehmer, et al.. X!TandemPipeline++: Software for Ion Mobility-Enabled Quantitative Proteomics in timsTOF Data Format. 70th ASMS Conference on Mass Spectrometry and Allied Topics ( ASMS 2022 ), Jun 2022, Minneapolis, United States. . ⟨hal-03687564⟩
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