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PXD033865

PXD033865 is an original dataset announced via ProteomeXchange.

Dataset Summary
Title29-Plex Tandem Mass Tag Mass Spectrometry Enabling Accurate Quantification by Interference Correction
DescriptionTandem mass tag (TMT) mass spectrometry is a mainstream isobaric chemical labeling strategy for profiling proteomes. Here we present a 29-plex TMT method to combine the 11-plex and 18-plex labeling strategies. The 29-plex method was examined with a pooled sample composed of 1x, 3x and 10x E. coli peptides with 100x human background peptides, which generated two E. coli datasets (TMT11 and TMT18), displaying the distorted ratios of 1.0:1.7:4.2 and 1.0:1.8:4.9, respectively. This ratio compression from the expected 1:3:10 ratios was caused by co-isolated TMT-labeled ions (i.e., noise). Interestingly, the mixture of two TMT sets produced MS/MS spectra with unique features for the noise detection: (i) in TMT11-labeled spectra, TMT18-specific reporter ions (e.g., 135N) were shown as the noise; (ii) in TMT18-labeled spectra, the TMT11/TMT18-shared reporter ions (e.g., 131C) typically exhibited higher intensities than TMT18-specific reporter ions, due to contaminated TMT11-labeled ions in these shared channels. We further estimated the noise levels contributed by both TMT11- and TMT18-labeled peptides, and corrected reporter ion intensities in every spectrum. Finally, the anticipated 1:3:10 ratios were largely restored. This strategy was also validated using another 29-plex sample with 1:5 ratios. Thus the 29-plex method expands the TMT throughput and enhances the quantitative accuracy.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:27:32.640.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterhuan sun
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListiodoacetamide derivatized residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-05-12 09:30:01ID requested
12023-03-10 10:49:31announced
22023-11-14 08:27:34announced2023-11-14: Updated project metadata.
Publication List
Sun H, Poudel S, Vanderwall D, Lee DG, Li Y, Peng J, 29-Plex tandem mass tag mass spectrometry enabling accurate quantification by interference correction. Proteomics, 22(19-20):e2100243(2022) [pubmed]
Keyword List
submitter keyword: mass spectrometry
liquid chromatography
proteomics
proteome
tandem mass tag
ratio compression
interference
data processing
Contact List
Junmin Peng
contact affiliationSt.jude children's research hospital
contact emailjunmin.peng@stjude.org
lab head
huan sun
contact affiliationSt.Jude Children's Research Hospital
contact emailhuansun0@gmail.com
dataset submitter
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