PXD029531

PXD029531 is an original dataset announced via ProteomeXchange.

Title	Increasing the throughput of sensitive proteomics by plexDIA
Description	Mass-spectrometry methods enable high-throughput proteomics with large input samples, but the depth and throughput of protein analysis remain limited for smaller samples. We aimed to increase throughput for analyzing limited samples while achieving high proteome coverage and quantitative accuracy. Thus, we developed a general experimental and computational framework, plexDIA, for simultaneously multiplexing the analysis of both peptides and samples. Multiplexed analysis with plexDIA increases throughput multiplicatively with the number of labels without reducing protein coverage or quantitative accuracy. Specifically, 3-plex nonisobaric labeling of sub-microgram samples increases the number of quantitative protein ratios by about 3-fold, enabling the quantification of over 25,000 protein data points per hour of active gradient on a first-generation Q Exactive instrument. Furthermore, plexDIA increases the consistency of protein detection and quantification across samples and reduces missing data by over 2-fold. We applied plexDIA to quantify proteome dynamics during the cell division cycle in cells isolated based on their DNA content. The high sensitivity and accuracy of plexDIA detected many classical cell cycle proteins and discovered new ones. These results establish a general framework for increasing the throughput of highly sensitive and quantitative protein analysis.
HostingRepository	MassIVE
AnnounceDate	2021-11-03
AnnouncementXML	Submission_2021-11-03_15:01:51.320.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jason Derks
SpeciesList	scientific name: Escherichia coli; common name: E. coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae; common name: baker's yeast; NCBI TaxID: 4932; scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	mTRAQ; mTRAQ:13C(3)15N(1); mTRAQ:13C(6)15N(2)
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-02 15:14:02	ID requested
⏵ 1	2021-11-03 15:01:51	announced

no publication

submitter keyword: plexDIA, DIA, mTRAQ, Cell cycle, high-throughput sensitive proteomics, multiplexing, nonisobaric labels, sub-microgram samples

Nikolai Slavov
contact affiliation	Northeastern University
contact email	n.slavov@northeastern.edu
lab head
Jason Derks
contact affiliation	Northeastern University
contact email	derks.j@northeastern.edu
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/MSV000088302/