PXD038383 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD038383
- Label: PRIDE project
- Name: Spin column-based prefractionation alternatives for Streamlined Tandem Mass Tag (SL-TMT) sample processing