PXD005984

PXD005984 is an original dataset announced via ProteomeXchange.

Title	Quantitative assessment of the effects of trypsin digestion methods on immunoprecipitation-mass spectrometry-based protein-protein interaction analysis
Description	Immunoprecipitation-mass spectrometry (IP-MS) has become the method of choice for discovering protein-protein interaction (PPI) under native conditions. The success of the IP-MS depends on the efficiency of trypsin digestion and recovery of the tryptic peptides for MS analysis. Several different protocols have been used for trypsin digestion of protein complexes in IP-MS studies, but no systematic studies have been conducted on the impact of trypsin digestion conditions on the identification of PPI. Here, we identified the interactome of transcription factor p65 (RelA) to test five distinct trypsin digestion methods (two using “on-bead”, two using “in-solution”, and one using “in-gel” protocols) and determined which method yielded the best interactome coverage. Our study indicates that high-abundance RelA interactors can be universally identified by all five methods, but the identification of low-abundance RelA interactors is significantly affected by the choice of trypsin digestion methods. We found that eluting RelA complex with sodium dodecyl sulfate (SDS) and followed by filter-aided sample preparation (FASP)/in-solution digestion is the best among the methods that were tested. We also found that different digestion protocols influences the selected reaction monitoring (SRM)-MS quantification of PPIs, suggesting that optimization of trypsin digestion condition may be required for robust study of targeted analysis of PPIs.
HostingRepository	PRIDE
AnnounceDate	2017-07-25
AnnouncementXML	Submission_2017-07-25_09:46:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yingxin Zhao
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-28 01:22:08	ID requested
⏵ 1	2017-07-25 09:46:01	announced

Zhang Y, Sun H, Zhang J, Brasier AR, Zhao Y, Quantitative Assessment of the Effects of Trypsin Digestion Methods on Affinity Purification-Mass Spectrometry-based Protein-Protein Interaction Analysis. J Proteome Res, 16(8):3068-3082(2017) [pubmed]

curator keyword: Technical

submitter keyword: RelA interactome, trypsin digestion, protein-protein interaction

Yingxin Zhao, Ph.D.
contact affiliation	University of Texas Medical Branch
contact email	yizhao@utmb.edu
lab head
Yingxin Zhao
contact affiliation	University of Texas Medical Branch
contact email	yizhao@utmb.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/2017/07/PXD005984

PRIDE project URI

• PRIDE
  1. PXD005984
     1. Label: PRIDE project
     2. Name: Quantitative assessment of the effects of trypsin digestion methods on immunoprecipitation-mass spectrometry-based protein-protein interaction analysis