PXD021187

PXD021187 is an original dataset announced via ProteomeXchange.

Title	A Versatile Isobaric Tag Enables Proteome Quantification in Data Dependent and Data Independent Acquisition Mode
Description	Quantifying proteins based on peptide-coupled reporter-ions is a leading multiplexed quantitative strategy in proteomics that significantly alleviates the problem of ratio distortion caused by peptide co-fragmentation, as commonly observed in other reporter-ion based approaches, such as TMT and iTRAQ. Fueled by improvements in mass spectrometry and data processing, data-independent acquisition (DIA) is an attractive alternative to data dependent acquisition (DDA) due to its better reproducibility. While multiplexed labeling is widely used in DDA, it is rarely used in DIA, presumably because current approaches lead to more complex MS2 spectra or to a reduction in quantification accuracy and precision. Herein, we present a versatile acetyl-alanine-glycine (Ac-AG) tag which conceals quantitative information in isobarically labeled peptides and reveals it upon tandem MS in the form of peptide-coupled reporter-ions. Since the peptide-coupled reporter-ion is precursor-specific while fragment ions of the peptide backbone originating from different labeling channels are same, the Ac-AG tag is compatible with both the widely adopted DDA as well as with the DIA mode. By isolating the monoisotopic peak of the precursor ion in DDA, intensities of the peptide-coupled reporter-ions simply represent the relative ratios between constituent samples. While in DIA, the ratio can be inferred after deconvoluting peptide-coupled reporter-ions. The proteome quantification capability of the Ac-AG tag was demonstrated by triplex labeling of a yeast proteome spiked with bovine serum albumin (BSA) over a 10-fold dynamic range. Within a complex proteomics background, the BSA spiked at 1:5:10 ratios was detected at ratios of 1.00 : 4.87 : 10.13 in DDA and 1.16 : 5.20 : 9.64 in DIA.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_09:10:39.336.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD021187
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Xiaobo Tian
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-28 03:53:12	ID requested
⏵ 1	2021-09-09 09:10:40	announced

Tian X, de Vries MP, Permentier HP, Bischoff R, A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes. Anal Chem, 92(24):16149-16157(2020) [pubmed]

submitter keyword: isobaric labeling, quantitative proteomics,data dependent acquisition,data-independent acquisition

Rainer Bischoff
contact affiliation	Department of Analytical Biochemistry, University of Groningen
contact email	r.p.h.bischoff@rug.nl
lab head
Xiaobo Tian
contact affiliation	University of Groningen
contact email	tianxiaobo002@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021187
     1. Label: PRIDE project
     2. Name: A Versatile Isobaric Tag Enables Proteome Quantification in Data Dependent and Data Independent Acquisition Mode