PXD038383

PXD038383 is an original dataset announced via ProteomeXchange.

Title	Spin column-based prefractionation alternatives for Streamlined Tandem Mass Tag (SL-TMT) sample processing
Description	Fractionation is essential to achieving deep proteome coverage for sample multiplexing experiments where currently up to 18 samples can be analyzed concurrently. However, prefractionation (i.e., upstream of LC-MS/MS analysis) with a liquid chromatography system constrains sample processing as only a single sample can be fractionated at once. Here, we highlight the use of spin column-based methods which permit multiple multiplexed samples to be prefractionated simultaneously. These methods require only a centrifuge and eliminate the need for a dedicated liquid chromatograph. We investigate prefractionation with strong anion exchange (SAX) and high-pH reversed phase (HPRP) spin columns, as well as a combination of both, as methods of prefractionation. In two separate experiments, we acquired deep proteome coverage (>8,000 quantified proteins), while starting with only 25 µg of protein per channel. Our datasets showcase the proteome alterations in two human cell lines resulting from treatment with inhibitors acting on the ubiquitin-proteasome system. We recommend this spin column-based prefractionation strategy for high-throughput screening applications or whenever a liquid chromatograph is not readily available.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:18:53.219.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joao Paulo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetic acid derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-26 03:55:03	ID requested
1	2023-12-28 11:16:48	announced
⏵ 2	2024-10-22 06:18:56	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2023.104839;

Liu X, Rossio V, Paulo JA, Spin column-based peptide fractionation alternatives for streamlined tandem mass tag (SL-TMT) sample processing. J Proteomics, 276():104839(2023) [pubmed]

submitter keyword: FAIMS, TMTpro, HPRP, isobaric tagging,SAX

Joao A. Paulo
contact affiliation	Department of Cell Biology Harvard Medical School 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/2023/12/PXD038383

PRIDE project URI

• PRIDE
  1. PXD038383
     1. Label: PRIDE project
     2. Name: Spin column-based prefractionation alternatives for Streamlined Tandem Mass Tag (SL-TMT) sample processing