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PXD029531 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIncreasing the throughput of sensitive proteomics by plexDIA
DescriptionMass-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.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJason 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;
ModificationListmTRAQ; mTRAQ:13C(3)15N(1); mTRAQ:13C(6)15N(2)
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-11-02 15:14:02ID requested
12021-11-03 15:01:51announced
Publication List
no publication
Keyword List
submitter keyword: plexDIA, DIA, mTRAQ, Cell cycle, high-throughput sensitive proteomics, multiplexing, nonisobaric labels, sub-microgram samples
Contact List
Nikolai Slavov
contact affiliationNortheastern University
contact emailn.slavov@northeastern.edu
lab head
Jason Derks
contact affiliationNortheastern University
contact emailderks.j@northeastern.edu
dataset submitter
Full Dataset Link List
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Dataset FTP location
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