MaxDIA enables library-based and library-free data-independent acquisition proteomics

MaxDIA enables library-based and library-free data-independent acquisition proteomics

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....

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Bibliographic Details
Published in:Nature biotechnology 2021-12, Vol.39 (12), p.1563-1573
Main Authors: Sinitcyn, Pavel, Hamzeiy, Hamid, Salinas Soto, Favio, Itzhak, Daniel, McCarthy, Frank, Wichmann, Christoph, Steger, Martin, Ohmayer, Uli, Distler, Ute, Kaspar-Schoenefeld, Stephanie, Prianichnikov, Nikita, Yılmaz, Şule, Rudolph, Jan Daniel, Tenzer, Stefan, Perez-Riverol, Yasset, Nagaraj, Nagarjuna, Humphrey, Sean J, Cox, Jürgen
Format: Article
Language:eng
Subjects:
Analysis
Coefficient of variation
Computer programs
Data analysis
Freight cars
Ionic mobility
Learning algorithms
Libraries
Machine learning
Matching
Methods
New technology
Peptide Library
Proteins
Proteome - analysis
Proteomes
Proteomics
Proteomics - methods
Software
Spectrometry
Workflow
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Description
Summary: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.
ISSN:1087-0156
1546-1696