PXD020815

PXD020815 is an original dataset announced via ProteomeXchange.

Title	HYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments
Description	Isobaric tagging is a powerful strategy for global proteome profiling. A caveat of isobaric tag-based quantification is “interference” which may be caused by co-eluting peptides that are co-isolated, co-fragmented, and co-analyzed, thereby confounding quantitative accuracy. Here, we present a two-proteome standard that challenges the mass spectrometer to measure a range of protein abundance ratios in a background of potential interference. The HYpro16 standard consists of TMTpro-labeled human peptides at a 1:1 ratio across all channels into which we spike TMTpro-labeled peptides in triplicate at 20:1, 10:1, 4:1, and 2:1 ratios. We showcase the HYpro16 standard by 1) altering the MS2 isolation window width and 2) using different data acquisition methods (hrMS2, SPS-MS3, RTS-MS3). Our data illustrate that wider isolation widths moderately increase TMT signal, the benefits of which are offset by decreased ratio accuracy. We also show that using real-time database searching (RTS)-MS3 resulted in the most accurate ratios. Additionally, the number of quantified yeast proteins using RTS-MS3 approaches that of hrMS2 when using a yeast-specific database for real-time searching. In short, this quality control standard allows for the assessment of multiple quantitative measurements within a single run which can be compared across instruments to benchmark and track performance.
HostingRepository	PRIDE
AnnounceDate	2021-08-16
AnnouncementXML	Submission_2021-08-16_00:24:32.668.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-09 23:33:56	ID requested
⏵ 1	2021-08-16 00:24:33	announced

Navarrete-Perea J, Gygi SP, Paulo JA, HYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments. J Am Soc Mass Spectrom, 32(1):247-254(2021) [pubmed]

submitter keyword: SPS-MS3, Multi-Notch, TMT, Lumos, standard, multiplex

Joao A. Paulo
contact affiliation	Department of 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. PXD020815
     1. Label: PRIDE project
     2. Name: HYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments