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PXD058918

PXD058918 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIsobaric Tagging and Data Independent Acquisition as Complementary Strategies for Proteome Profiling on an Orbitrap Astral Mass Spectrometry
DescriptionComprehensive global proteome profiling that is amenable to high throughput processing will broaden our understanding of complex biological systems. Here, we evaluated two leading mass spectrometry techniques—Data-Independent Acquisition (DIA) and Tandem Mass Tagging (TMT)—for extensive protein abundance profiling. DIA provides label-free quantification with a broad dynamic range, while TMT enables multiplexed analysis using isobaric tags for efficient cross-sample comparisons. We analyzed 18 samples, including four cell lines (IHCF, HCT116, HeLa, MCF7) under standard growth conditions, in addition to IHCF treated with two H₂O₂ concentrations, all in triplicate. Experiments were conducted on an Orbitrap Astral mass spectrometer, employing Field Asymmetric Ion Mobility Spectrometry (FAIMS). Despite utilizing different acquisition strategies, both the DIA and TMT approaches achieved comparable proteome depth and quantitative consistency, with each method quantifying over 10,000 proteins across all samples, with slightly more protein-level precision for the TMT strategy. Relative abundance correlation analysis showed strong agreement at both peptide and protein levels. Our findings highlight the complementary strengths of DIA and TMT for high-coverage proteomic studies, providing flexibility in method selection based on specific experimental needs.
HostingRepositoryPRIDE
AnnounceDate2025-02-14
AnnouncementXMLSubmission_2025-02-14_12:31:16.362.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJoao Paulo
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue
InstrumentOrbitrap Astral
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-12-16 18:28:27ID requested
12025-02-14 12:31:16announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: FAIMS, DIA, Astral, IHCF,TMTpro
Contact List
Joao A. Paulo
contact affiliationDepartment of Cell Biology Harvard Medical School Boston, MA, USA
contact emailjoao_paulo@hms.harvard.edu
lab head
Joao Paulo
contact affiliationHarvard Medical School
contact emailjoao_paulo@post.harvard.edu
dataset submitter
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Dataset FTP location
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