PXD002021

PXD002021 is an original dataset announced via ProteomeXchange.

Title	Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry
Description	The generation of dynamic models of biological processes critically depends on the determination of precise cellular concentrations of biomolecules. Measurements of system-wide absolute protein levels are particularly valuable information in systems biology. Recently, mass spectrometry based proteomics approaches have been developed to estimate protein concentrations on a proteome-wide scale. However, for very complex proteomes, fractionation steps are required, increasing samples number and instrument analysis time. As a result, the number of full proteomes that can be routinely analyzed is limited. Here we combined absolute quantification strategies with the multiplexing capabilities of isobaric tandem mass tags to determine cellular protein abundances in a high throughput and proteome-wide scale even for highly complex biological systems, such as a whole human cell line. We generated two independent data sets to demonstrate the power of the approach regarding sample throughput, dynamic range, quantitative accuracy and proteome coverage in comparison to existing mass spectrometry based strategies.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_10:02:13.636.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002021
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Schizosaccharomyces pombe; NCBI TaxID: 4896; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-04-07 05:31:45	ID requested
⏵ 1	2024-10-07 10:02:14	announced

Dreier RF, Ahrn, é E, Broz P, Schmidt A, Global Ion Suppression Limits the Potential of Mass Spectrometry Based Phosphoproteomics. J Proteome Res, 18(1):493-507(2019) [pubmed]

10.6019/PXD002021;

10.1021/acs.jproteome.8b00812;

curator keyword: Technical

submitter keyword: HEK cells, TMT,S. Pombe, iBAQ, absolute quantification

Alexander Schmidt
contact affiliation	University of Basel, Biozentrum, 4056 Basel, Switzerland
contact email	alex.schmidt@unibas.ch
lab head
Alexander Schmidt
contact affiliation	Proteomics Core Facility
contact email	alex.schmidt@unibas.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002021
     1. Label: PRIDE project
     2. Name: Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry