PXD016613

PXD016613 is an original dataset announced via ProteomeXchange.

Title	Bait correlation improves interactor identification by TMT-AP-MS
Description	The quantitative multiplexing capacity of isobaric Tandem Mass Tags (TMT) has increased the throughput of affinity purification mass spectrometry (AP-MS) to characterize protein interaction networks of immunoprecipitated baits. However, variable bait levels between replicates can convolute interactor identification. We compared the Student's t difference test and Pearson's R correlation as methods to generate t-statistics and assessed the significance of interactors following TMT-AP-MS. Using a simple linear model of protein recovery in immunoprecipitates to simulate reporter ion ratio distributions, we found that correlation-derived t-statistics protect against bait variance while robustly controlling Type I errors (false positives). We experimentally determined the performance of these two approaches for determining t-statistics under two experimental conditions: irreversible prey association to the Hsp40 mutant DNAJB8H31Q followed by stringent washing, and reversible association to 14 3 3 with gentle washing. Correlation-derived t-statistics performed at least as well as difference test t-statistics for each sample, with substantial improvement in performance for experiments with high bait level variance. Deliberately varying bait levels over a large range fails to improve selectivity but does increase robustness between runs. The use of correlation-derived t-statistics should improve identification of interactors using TMT-AP-MS.
HostingRepository	PRIDE
AnnounceDate	2020-06-22
AnnouncementXML	Submission_2020-06-21_17:12:45.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD016613
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Joseph Genereux
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-05 03:06:56	ID requested
⏵ 1	2020-06-21 17:12:46	announced

Mei L, Montoya MR, Quanrud GM, Tran M, Villa-Sharma A, Huang M, Genereux JC, Bait Correlation Improves Interactor Identification by Tandem Mass Tag-Affinity Purification-Mass Spectrometry. J Proteome Res, 19(4):1565-1573(2020) [pubmed]

submitter keyword: AP-MS, TMT, Protein-protein interactions

Joseph Genereux
contact affiliation	Department of Chemistry, University of California, Riverside 501 Big Springs Rd, Riverside, CA 92521
contact email	josephg@ucr.edu
lab head
Joseph Genereux
contact affiliation	University of California, Riverside
contact email	josephg@ucr.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016613
     1. Label: PRIDE project
     2. Name: Bait correlation improves interactor identification by TMT-AP-MS