Updated MS²PIP web server supports cutting-edge proteomics applications - Archive ouverte HAL
Article Dans Une Revue Nucleic Acids Research Année : 2023

Updated MS²PIP web server supports cutting-edge proteomics applications

Arthur Declercq
Cristina Chiva

Résumé

Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past year s, especiall y for applications in challenging proteomics identification workflows such as immunopeptidomics and the full-proteome identification of data independent acquisition spectra. Since its inception, the MS 2 PIP peptide spectrum predictor has been widely used f or v arious do wnstream applications, mostl y thanks to its accuracy, ease-of-use, and broad applicability. We here present a thoroughly updated version of the MS 2 PIP web server, which includes new and more performant prediction models for both trypticand non-tryptic peptides, for immunopeptides, and for CID-fragmented TMT-labeled peptides. Additionall y, we ha ve also added ne w functionality to greatl y facilitate the generation of proteome-wide predicted spectral libraries, requiring only a FASTA protein file as input. These libraries also include retention time predictions from DeepLC. Moreover, we now pr o vide pre-b uilt and read y-to-do wnload spectral libraries f or v arious model organisms in multiple DIAcompatible spectral library formats. Besides upgrading the back-end models, the user experience on the MS 2 PIP web server is thus also greatly enhanced, extending its applicability to new domains, including immunopeptidomics and MS3-based TMT quantification experiments. MS 2 PIP is freely available at https:// iomics.ugent.be/ ms2pip/ .

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Dates et versions

hal-04745830 , version 1 (21-10-2024)

Identifiants

Citer

Arthur Declercq, Robbin Bouwmeester, Cristina Chiva, Eduard Sabidó, Aurélie Hirschler, et al.. Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Research, 2023, 51, pp.W338 - W342. ⟨10.1093/nar/gkad335⟩. ⟨hal-04745830⟩
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