PXD018589

PXD018589 is an original dataset announced via ProteomeXchange.

Title	SMD-IPTL 4-plex yeast and BSA-yeast
Description	Isobaric peptide termini labeling (IPTL) is an attractive protein quantification method, because it provides more accurate and reliable quantification information than traditional isobaric labelling methods (TMT, iTRAQ) by making use of the entire fragment ion series instead of only a single reporter ion. The multiplexing capacity of published IPTL implementations is, however, limited to three. Here, we present a selective maleylation-directed isobaric peptide termini labelling (SMD-IPTL) approach for quantitative proteomics of LysC protein digests. SMD-IPTL extends the multiplexing capacity to 4-plex with the potential for higher levels of multiplexing using commercially available 13C/15N-labelled amino acids. SMD-IPTL is achieved in a one-pot reaction in three consecutive steps: 1) selective maleylation at the N-terminus; 2) labelling at the ԑ-NH2 group of the C-terminal Lys with isotopically labelled acetyl alanine; 3) thiol Michael addition of an isotopically labelled acetyl cysteine at the maleylated N-terminus. The isobarically labelled peptides are fragmented into sets of b- and y-ion clusters upon LC-MS/MS, which not only convey sequence information but also quantitative information for every labelling channel and avoid the issue of ratio distortion observed with reporter-ion-based approaches. We demonstrate the SMD-IPTL approach with a 4-plex labelled sample of BSA and yeast lysates mixed at different ratios. Utilizing SMD-IPTL for labelling and a narrow precursor isolation window of 0.8 Th with an offset of -0.2 Th, accurate ratios were measured across a 10-fold mixing range of BSA in a background of yeast proteome. With the yeast proteins mixed at ratios of 1:5:1:5, BSA was detected at ratios 0.94:2.46:4.70:9.92 when spiked at 1:2:5:10 ratios with an average standard deviation of peptide ratios of 0.34.
HostingRepository	PRIDE
AnnounceDate	2020-04-27
AnnouncementXML	Submission_2020-04-27_00:07:12.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD018589
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	Oxidation; monohydroxylated residue; Carbamidomethyl; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-15 15:54:15	ID requested
⏵ 1	2020-04-27 00:07:13	announced

Tian X, de Vries MP, Visscher SWJ, Permentier HP, Bischoff R, Selective Maleylation-Directed Isobaric Peptide Termini Labeling for Accurate Proteome Quantification. Anal Chem, 92(11):7836-7844(2020) [pubmed]

submitter keyword: SMD-IPTL

Rainer Bischoff
contact affiliation	University of Groningen, Department of > Analytical Biochemistry
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. PXD018589
     1. Label: PRIDE project
     2. Name: SMD-IPTL 4-plex yeast and BSA-yeast