PXD022589

PXD022589 is an original dataset announced via ProteomeXchange.

Title	MaxDIA enables highly sensitive and accurate library-based and library-free data-independent acquisition proteomics (DIA data)
Description	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.
HostingRepository	PRIDE
AnnounceDate	2021-07-12
AnnouncementXML	Submission_2021-07-11_22:12:57.481.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yasset Perez-Riverol
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF; TripleTOF 5600; 6520A Quadrupole Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-17 08:52:17	ID requested
1	2021-07-11 22:06:31	announced
⏵ 2	2021-07-11 22:12:58	announced	2021-07-12: Updated publication reference for PubMed record(s): 34239088.

Sinitcyn P, Hamzeiy H, Salinas Soto F, Itzhak D, McCarthy F, Wichmann C, Steger M, Ohmayer U, Distler U, Kaspar-Schoenefeld S, Prianichnikov N, Y, ı, lmaz Ş, Rudolph JD, Tenzer S, Perez-Riverol Y, Nagaraj N, Humphrey SJ, Cox J, MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nat Biotechnol, 39(12):1563-1573(2021) [pubmed]

submitter keyword: MaxQuant, Benchmark

Jurgen Cox
contact affiliation	Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
contact email	cox@biochem.mpg.de
lab head
Yasset Perez-Riverol
contact affiliation	EBI
contact email	yperez@ebi.ac.uk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD022589

PRIDE project URI

• PRIDE
  1. PXD022589
     1. Label: PRIDE project
     2. Name: MaxDIA enables highly sensitive and accurate library-based and library-free data-independent acquisition proteomics (DIA data)