A sample-aware diaPASEF method optimization strategy for a timsTOF platform that demonstrates the most substantial impact on low-abundance proteins and provides an opportunity for a more precise and comprehensive analysis of the biological functions of biomarkers.
J. Rijal, Imane Charmarke Askar, Aurélie Hirschler et al.· Analytical Chemistry· 0 citations
OmicsFM, a modality-agnostic transformer pretrained through masked abundance reconstruction on an unprecedented proteomics data corpus of 48,837 quality-filtered proteomics profiles from 1,397 reprocessed PRIDE projects, firmly establishes the possibility of training highly performant proteomics-based foundation models...
Sander Heyndrickx, R. Gabriels, Harikrishnan Ramadasan et al.· bioRxiv· 1 citation
The potential for open modification searching to correct potential mistakes in non-canonical proteins detection by preventing modified canonical peptides or variants from being incorrectly identified as non-canonical peptides is shown.
V. Vasylieva, Enrico Massignani, Tine Claeys et al.· bioRxiv· 0 citations
Scop3P-Toolkit is an open-source executable analytical environment for interactive analysis of PTMs, mutations, and proteomics-derived peptides in their structural context, providing transparent, accessible, and reproducible workflows for both computational and experimental researchers.
Adrián Díaz, Natalia Tichshenko, Boris Depoortere et al.· bioRxiv· 0 citations
A major update of Scop3P, a proteomics-informed knowledgebase that contextualizes human phosphorylation sites within integrated sequence, structural, biophysical, evolutionary, and mutational frameworks, and provides a scalable and provenance-aware resource for phosphosite interpretation, hypothesis generation, and dat...
P. Ramasamy, Natalia Tichshenko, Adrián Díaz et al.· bioRxiv· 0 citations
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