Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides

Autor: Grégoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella, Mélisande Blein-Nicolas, Virginie Lollier, Emile Benoist, Géraldine Jean, Guillaume Fertin, Hélène Rogniaux, Dominique Tessier

Publikováno v: BMC Bioinformatics, Vol 24, Iss 1, Pp 1-17 (2023)

Abstract Background In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a limited number of fal

Externí odkaz: https://doaj.org/article/e557a1cbf29a4f44a25e328306201caf

SpecGlob: rapid and accurate alignment of mass spectra differing from their peptide models by several unknown modifications

Autor: Albane Lysiak, Guillaume Fertin, Géraldine Jean, Dominique Tessier

BackgroundIn proteomics, mass spectra representing peptides carrying multiple unknown modifications are particularly difficult to interpret, which results in a large number of unidentified spectra.MethodsWe developed SpecGlob, a dynamic programming a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0463d046b5993c3906e0e9fbf4a04570
https://doi.org/10.1101/2022.05.31.494131

Evaluation of open search methods based on theoretical mass spectra comparison

Autor: Guillaume Fertin, Géraldine Jean, Dominique Tessier, Albane Lysiak

Publikováno v: BMC Bioinformatics
BMC Bioinformatics, BioMed Central, 2021, 22 (2 (Special Issue)), pp.65. ⟨10.1186/s12859-021-03963-6⟩
BMC Bioinformatics, Vol 22, Iss S2, Pp 1-17 (2021)
BMC Bioinformatics, BioMed Central, 2021, 22 (S2), pp.104-120. ⟨10.1186/s12859-021-03963-6⟩

Background Mass spectrometry remains the privileged method to characterize proteins. Nevertheless, most of the spectra generated by an experiment remain unidentified after their analysis, mostly because of the modifications they carry. Open Modificat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2b100aea7596d2b472676874bd7a9971
https://hal.inrae.fr/hal-03318623