PXD043778-1

PXD043778 is an original dataset announced via ProteomeXchange.

Title	Overcoming the detrimental O-acylation in TMTpro labeling improves the proteome depth and quantification precision.
Description	The advent of TMTpro reagents expands the sample multiplexing capacity and enables quantification of up to 18 samples in a multiplexed manner. Similar to classic TMT reagents, TMTpro reagents contain a tertiary amine group in their mole-cules, which markedly enhances their reactivity toward hydroxyl groups and thus results in overlabeling of serine, threo-nine and tyrosine residues. Overlabeling significantly compromises the proteome analysis in terms of sensitivity and precision. Here, we report a novel TMTpro labeling method that overcomes the detrimental overlabeling while delivering efficient labeling for amines. Additionally, our method is cost-effective as it requires only half the amount of TMTpro reagents recommended by the reagent manufacturer. We compared our method with the standard method (provided by the TMTpro manufacturer) in a deep-scale analysis of a yeast/human two-proteome model sample. Even at the depth of over 10000 proteins, our method detected 36.2% more unique peptides and 11.5% more protein groups than the standard method. Moreover, our method considerably improves the quantitative precision due to the reduced variability in label-ing and increased protein sequence coverage. This substantially enhanced the statistical power of our method for detect-ing differentially abundant proteins, providing an average of 16% more yeast proteins reaching statistical significance.
HostingRepository	iProX
AnnounceDate	2023-12-19
AnnouncementXML	Submission_2024-04-27_22:39:40.188.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yan Cai
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-13 22:11:45	ID requested
⏵ 1	2024-04-27 22:39:41	announced

Cai Y, Chang C, Liao R, Overcoming the detrimental O-acylation in TMTpro labeling improves the proteome depth and quantification precision. Anal Chim Acta, 1304():342538(2024) [pubmed]

submitter keyword: Proteomics, TMTpro, LC-MS/MS

Rijing Liao
contact affiliation	Shanghai Institute of Precision Medicine, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine
contact email	rjliao@shsmu.edu.cn
lab head
Yan Cai
contact affiliation	Shanghai Ninth People ‘s Hospital
contact email	caiyan0723@shsmu.edu.cn
dataset submitter

iProX dataset URI