MaxDIA enables library-based and library-free data-independent acquisition proteomics.
Journal
Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648
Informations de publication
Date de publication:
12 2021
12 2021
Historique:
received:
17
11
2020
accepted:
27
05
2021
pubmed:
10
7
2021
medline:
20
4
2022
entrez:
9
7
2021
Statut:
ppublish
Résumé
MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.
Identifiants
pubmed: 34239088
doi: 10.1038/s41587-021-00968-7
pii: 10.1038/s41587-021-00968-7
pmc: PMC8668435
doi:
Substances chimiques
Peptide Library
0
Proteome
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1563-1573Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/P024599/1
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2021. The Author(s).
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