Using ProteoCombiner to integrate bottom-up and top-down proteomics data to improve proteoform identification

Diogo Borges Lima (1) , Mathieu Dupré (1) , Magalie Duchateau (2) , Quentin Giai Gianetto (2, 3) , Martial Jean-Pierre Rey (1) , Mariette I Matondo (2) , Julia Chamot-Rooke (1)

1 UTechS MSBio - Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology
2 Plateforme de Protéomique / Proteomics platform
3 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB

Here we present a high-performance software for proteome analysis that combines different mass spectrometric approaches, such as, top-down for intact protein analyses and bottom-up, for proteolytic fragment characterization. ProteoCombiner capitalizes on the data arising from different experiments and proteomics search engines and presents the results in a user-friendly manner. Our tool also provides a rapid and easy visualization, manual validation and comparison of the identified proteoform sequences, including post-translational modifications (PTM) characterization. Thus, ProteoCombiner is recommended for studies dealing with different proteomics strategies, in order to increase confidence in proteoform identification including PTMs.

Keywords: proteomics; bioinformatics; top-down; bottom-up; mass spectrometry

Domains: Computer Science [cs]; Bioinformatics [q-bio.QM]; Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]

Diogo Borges Lima, Mathieu Dupré, Magalie Duchateau, Quentin Giai Gianetto, Martial Jean-Pierre Rey, et al.. Using ProteoCombiner to integrate bottom-up and top-down proteomics data to improve proteoform identification. 2021. ⟨pasteur-03243560⟩