PXD003346-1

PXD003346 is an original dataset announced via ProteomeXchange.

Title	Ratio accuracy evaluation and correction using tandem mass tags
Description	The multiplexing capabilities of isobaric mass tag based protein quantification, such as Tandem Mass Tags (TMT) or Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) have dramatically increased the scope of Mass Spectrometry (MS) based proteomics studies. Not only does the technology allow for the simultaneous quantification of multiple samples in a single MS injection, but its seamless compatibility with extensive sample pre-fractionation methods allow for comprehensive study of complex proteomes. However, reporter ion based quantification has often been criticized for limited quantification accuracy due to interference from co-eluting peptides and peptide fragments. In this study, we investigate the extent of this problem and propose an effective and easy-to-implement remedy relying on spiking a 6-protein calibration mixture to the samples subject to relative quantification. Our ratio adjustment approach was evaluated on a large scale TMT 10-plex dataset derived from cancer cell lines with chromosome instability. Furthermore, we analyzed a complex 2-proteome artificial sample mixture and investigated the precision of TMT and precursor ion intensity based Label Free Quantification. Comparing the two methods we observed that the isobaric tag based quantification workflow, due to its superior precision, was able to confirm more and smaller protein abundance changes, at a fixed False Positive Rate.
HostingRepository	PRIDE
AnnounceDate	2016-07-01
AnnouncementXML	Submission_2016-07-01_00:55:14.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD003346
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Schmidt
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Oxidation; Carbamidomethyl
Instrument	Q Exactive; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-12-15 02:07:39	ID requested
⏵ 1	2016-07-01 00:55:16	announced

Ahrn, é E, Glatter T, Vigan, ò C, Schubert Cv, Nigg EA, Schmidt A, Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments. J Proteome Res, 15(8):2537-47(2016) [pubmed]

curator keyword: Technical

submitter keyword: Tandem mass tags, quantitative mass spectrometry, HCD, label-free quantification

Alexander Schmidt
contact affiliation	Biozentrum, Universtiy of Basel, 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. PXD003346
     1. Label: PRIDE project
     2. Name: Ratio accuracy evaluation and correction using tandem mass tags