PXD011009

PXD011009 is an original dataset announced via ProteomeXchange.

Title	Limits for resolving isobaric tandem mass tag reporter ions using phase constrained spectrum deconvolution
Description	A popular method for peptide quantification relies on isobaric labeling such as tandem mass tags (TMT) which enables multiplexed proteome analyses. Quantification is achieved by reporter ions generated by fragmentation in a tandem mass spectrometer. However, with higher degrees of multiplexing, the smaller mass differences between the reporter ions increase the mass resolving power requirements. This contrasts with faster peptide sequencing capabilities enabled by lowered mass resolution on Orbitrap instruments. It is therefore important to determine the mass resolution limits for highly multiplexed quantification when maximizing proteome depth. Here we defined the lower boundaries for resolving TMT reporter ions with 0.0063 Da mass differences using an ultra-high-field Orbitrap mass spectrometer. We found the optimal method depends on the relative ratio between closely spaced reporter ions and that 64 ms transient acquisition time provided sufficient resolving power for separating TMT reporter ions with absolute ratio changes up to 16-fold. Furthermore, a 32 ms transient processed with phase-constrained spectrum deconvolution provides >50% more identifications with >99% quantified, but with a slight loss in quantification precision and accuracy. These findings should guide decisions on what Orbitrap resolution settings to use in future proteomics experiments relying on isobaric TMT reporter ion quantification.
HostingRepository	PRIDE
AnnounceDate	2018-10-05
AnnouncementXML	Submission_2018-10-05_07:32:33.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Kelstrup
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-05 05:29:09	ID requested
⏵ 1	2018-10-05 07:32:34	announced

Kelstrup CD, Aizikov K, Batth TS, Kreutzman A, Grinfeld D, Lange O, Mourad D, Makarov AA, Olsen JV, Limits for Resolving Isobaric Tandem Mass Tag Reporter Ions Using Phase-Constrained Spectrum Deconvolution. J Proteome Res, 17(11):4008-4016(2018) [pubmed]

curator keyword: Technical

submitter keyword: quantitative proteomics, tmt, resolution, Q Exactive HF-X, phase constrained spectrum deconvolution

Jesper V. Olsen
contact affiliation	The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
contact email	jesper.olsen@cpr.ku.dk
lab head
Christian Kelstrup
contact affiliation	University of Copenhagen
contact email	chdake@cpr.ku.dk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011009
     1. Label: PRIDE project
     2. Name: Limits for resolving isobaric tandem mass tag reporter ions using phase constrained spectrum deconvolution