PXD011653

PXD011653 is an original dataset announced via ProteomeXchange.

Title	TKO6: A Peptide Standard to Assess Interference for Unit-Resolved Isobaric Labeling Platforms
Description	Protein abundance profiling using isobaric labeling is a well-established quantitative mass spectrometry technique. However, ratio distortion resulting from co-isolated and co-fragmented ions - commonly referred to as interference - remains a caveat of this technique. Tribrid mass spectrometers, such as the Orbitrap Fusion and the Orbitrap Fusion Lumos with a triple mass analyzer configuration, facilitate methods (namely SPS-MS3) that can help alleviate interference. Yet, few standards are available to measure interference. Here we introduce the TKO6 standard that assesses ion interference and is designed specifically for data acquired at low (unit) mass resolution. We use TKO6 to compare the degree of interference in MS2 versus MS3-based quantitation methods, data acquisition methods of different lengths, and ion trap-based TMT reporter ion analysis (IT-MS3). We show that the TKO6 standard is a valuable tool for assessing data quality and is particularly useful for benchmarking ion trap-based SPS-MS3 analyses.
HostingRepository	PRIDE
AnnounceDate	2019-03-07
AnnouncementXML	Submission_2019-03-07_08:01:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-12 02:11:50	ID requested
⏵ 1	2019-03-07 08:01:20	announced

Paulo JA, Navarrete-Perea J, Guha Thakurta S, Gygi SP, TKO6: A Peptide Standard To Assess Interference for Unit-Resolved Isobaric Labeling Platforms. J Proteome Res, 18(1):565-570(2019) [pubmed]

curator keyword: Technical

submitter keyword: TKO

interference

TMT

iTRAQ

SPS-MS3

Joao A. Paulo
contact affiliation	Cell Biology, Harvard Medical School, USA
contact email	joao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliation	Harvard Medical School
contact email	joao_paulo@post.harvard.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011653
     1. Label: PRIDE project
     2. Name: TKO6: A Peptide Standard to Assess Interference for Unit-Resolved Isobaric Labeling Platforms