⮝ Full datasets listing

PXD038383

PXD038383 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSpin column-based prefractionation alternatives for Streamlined Tandem Mass Tag (SL-TMT) sample processing
DescriptionFractionation 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:18:53.219.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJoao Paulo
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetic acid derivatized residue
InstrumentOrbitrap Eclipse
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-11-26 03:55:03ID requested
12023-12-28 11:16:48announced
22024-10-22 06:18:56announced2024-10-22: Updated project metadata.
Publication List
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]
Keyword List
submitter keyword: FAIMS, TMTpro, HPRP, isobaric tagging,SAX
Contact List
Joao A. Paulo
contact affiliationDepartment of Cell Biology Harvard Medical School Boston, MA, USA
contact emailjoao_paulo@post.harvard.edu
lab head
Joao Paulo
contact affiliationHarvard Medical School
contact emailjoao_paulo@post.harvard.edu
dataset submitter
Full Dataset Link List
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
Repository Record List
[ + ]