PXD029458

PXD029458 is an original dataset announced via ProteomeXchange.

Title	Assessing Interference in Isobaric Tag-based Sample Multiplexing using an 18-plex Interference Standard
Description	Reporter ion interference remains a limitation of isobaric tag-based sample multiplexing. Advances in instrumentation and data acquisition modes, such as the recently developed real-time database search (RTS), can reduce interference. However, interference persists as does the need to benchmark upstream sample preparation and data acquisition strategies. Here, we present an updated Triple yeast KnockOut (TKO) standard as well as corresponding upgrades to the TKO Viewing Tool (TVT2.5, http://tko.hms.harvard.edu/). Specifically, we expand the TKO standard to incorporate the TMTpro18-plex reagents (TKO18). We also construct a variant thereof which has been digested only with LysC (TKO18L). We compare proteome coverage and interference levels of TKO18 and TKO18L data that were acquired under different data acquisition modes and analyzed using TVT2.5. Our data illustrate that RTS reduces interference while improving proteome coverage and suggest that digesting with LysC alone only modestly reduces interference, albeit at the expense of proteome depth. Collectively, the two new TKO standards coupled with the updated TVT represent a convenient and versatile platform for assessing and developing methods to reduce interference in isobaric tag-based experiments.
HostingRepository	PRIDE
AnnounceDate	2022-01-06
AnnouncementXML	Submission_2022-01-06_08:54:03.430.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-01 04:59:47	ID requested
⏵ 1	2022-01-06 08:54:04	announced

Navarrete-Perea J, Liu X, Rad R, Gygi JP, Gygi SP, Paulo JA, Assessing interference in isobaric tag-based sample multiplexing using an 18-plex interference standard. Proteomics, 22(7):e2100317(2022) [pubmed]

submitter keyword: SPS-MS3, RTS, IFI, TMTpro18, Eclipse, FAIMS

Joao A. Paulo
contact affiliation	Department of Cell Biology Harvard Medical School Boston, MA 02115
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/2022/01/PXD029458

PRIDE project URI

• PRIDE
  1. PXD029458
     1. Label: PRIDE project
     2. Name: Assessing Interference in Isobaric Tag-based Sample Multiplexing using an 18-plex Interference Standard