Dataset Information

MaxDIA enables highly sensitive and accurate library-based and library-free data-independent acquisition proteomics (DIA data)

ABSTRACT: MaxDIA is a universal platform for analyzing data-independent acquisition proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves cutting-edge proteome coverage with significantly better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate estimates on both library-to-DIA match and protein levels, also when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA – a framework for the 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 novel 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.

INSTRUMENT(S): TripleTOF 5600, 6520 Quadrupole Time-of-Flight LC/MS, Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Escherichia Coli Candida Albicans (yeast)

SUBMITTER: Yasset Perez-Riverol

LAB HEAD: Jurgen Cox

PROVIDER: PXD022589 | Pride | 2021-07-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20190914_HFX4_SeHu_HeLa-400ng_DIA-GradientTest_120min_1.raw	Raw
	20190914_HFX4_SeHu_HeLa-400ng_DIA-GradientTest_120min_2.raw	Raw
	20190914_HFX4_SeHu_HeLa-400ng_DIA-GradientTest_30min_1.raw	Raw
	20190914_HFX4_SeHu_HeLa-400ng_DIA-GradientTest_30min_2.raw	Raw
	20190914_HFX4_SeHu_HeLa-400ng_DIA-GradientTest_60min_1.raw	Raw

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

Sinitcyn Pavel P Hamzeiy Hamid H Salinas Soto Favio F Itzhak Daniel D McCarthy Frank F Wichmann Christoph C Steger Martin M Ohmayer Uli U Distler Ute U Kaspar-Schoenefeld Stephanie S Prianichnikov Nikita N Yılmaz Şule Ş Rudolph Jan Daniel JD Tenzer Stefan S Perez-Riverol Yasset Y Nagaraj Nagarjuna N Humphrey Sean J SJ Cox Jürgen J

Nature biotechnology 20210708 12

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 fo ...[more]

PMID: 34239088

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