PXD023203

PXD023203 is an original dataset announced via ProteomeXchange.

Title	Strain-specific peptide (SSP) standard: A genetically encoded quality control standard for isobaric tagging strategies
Description	Isobaric tag-based sample multiplexing strategies are extensively used for global protein abundance profiling. However, such analyses are often confounded by ratio compression resulting from the co-isolation, co-fragmentation, and co-quantification of co-eluting peptides, termed “interference.” Recent analytical strategies incorporating ion mobility and real-time database searching have helped to alleviate interference, yet further assessment is needed. Here, we present the Strain-Specific Peptide (SSP) standard, a TMTpro-tagged reference sample that leverages the genetic variation in the proteomes of eight phylogenetically divergent mouse strains. Typically, a peptide with a missense mutation will have a different mass and retention time than the reference or native peptide. TMT reporter ion signal for the native peptide in strains that encode the mutant peptide suggests interference which can be quantified and assessed using the interference-free index (IFI). We showcase the SSP standard by investigating interference in three common data acquisition methods and by testing the improvements in the IFI when using ion mobility-based gas phase fractionation. In addition, we provide a user-friendly, online viewer to visualize the data and streamline calculation of the IFI. The SSP standard will aid in developing and optimizing isobaric tag-based experiments.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:20:43.425.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-17 11:06:37	ID requested
1	2021-04-03 11:08:33	announced
⏵ 2	2024-10-22 05:20:44	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.0c05483;

Zhang T, Keele GR, Churchill GA, Gygi SP, Paulo JA, Strain-Specific Peptide (SSP) Interference Reference Sample: A Genetically Encoded Quality Control for Isobaric Tagging Strategies. Anal Chem, 93(12):5241-5247(2021) [pubmed]

submitter keyword: TMTpro16, FAIMS, Eclipse, RTS-MS3,SPS-MS3, Founder Strains

Joao A. Paulo
contact affiliation	Harvard Medical School Cell Biology Boston, MA, 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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/04/PXD023203

PRIDE project URI

• PRIDE
  1. PXD023203
     1. Label: PRIDE project
     2. Name: Strain-specific peptide (SSP) standard: A genetically encoded quality control standard for isobaric tagging strategies