PXD001111-2

PXD001111 is an original dataset announced via ProteomeXchange.

Title	Combining solid phase extraction with ultra-short gradients in LC-MS/MS substantially improves protein identification per unit of time
Description	Here, we describe a novel LC system enabling rapid protein/proteome analysis which requires <10 min analysis time. The setup consists of an autosampler harbouring two sets of 96 STAGE-tips which function as pre-columns, and a short RP analytical column, which can run a 5 min gradient. We show that the system allows the efficient combination with several popular off-line pre-fractionation methods, such as gel-electrophoresis, strong-cation exchange chromatography, but also in the analysis of interactomes obtained by affinity purification. A typical shotgun proteomics experiment, involving 36 SCX fractions of an AspN digested cell lysate, lead to the detection of over 3600 protein groups in only 3h cumulative gradient time when using a QExactive mass analyser. Application to typical various proteomics experiments such as samples from pull-downs allowed the detection of hundreds of proteins whereby a given protein’s interactome could be determined in less than 1h of accumulated gradient time. This new LC system diminishes proteome analysis time considerably, whole providing sufficient proteomic detail, and may thus also aid in bringing proteomics into the clinic where fast turn-over times are essential.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:05:59.324.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	N. Binai
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2014-07-08 01:15:28	ID requested
1	2014-12-12 06:00:53	announced
⏵ 2	2024-10-22 04:06:00	announced	2024-10-22: Updated project metadata.

Binai NA, Marino F, Soendergaard P, Bache N, Mohammed S, Heck AJ, Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/MS system. J Proteome Res, 14(2):977-85(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: Hela, AP-MS, 2D, Jurkat, SPE-LC, E.coli

Albert Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University
contact email	A.J.R.Heck@uu.nl
lab head
N. Binai
contact affiliation	Faculty of Science
contact email	n.a.binai@uu.nl
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/2014/12/PXD001111

PRIDE project URI

• PRIDE
  1. PXD001111
     1. Label: PRIDE project
     2. Name: Combining solid phase extraction with ultra-short gradients in LC-MS/MS substantially improves protein identification per unit of time