PXD037946
PXD037946 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Pan-cancer plasma proteome profiling using SIS recombinant protein fragments reveals downregulation of proteins interacting with immunoglobulins in multiple myeloma |
Description | Mass spectrometry based on Data Independent Acquisition (DIA) strategies has developed into powerful tools suitable for precision medicine applications. Assays performed in this setting provide confident protein identification and precise quantification on an absolute scale when combined with stable isotope recombinant protein standards. Here, we describe a comprehensive targeted proteomics approach to profile a pan-cancer cohort consisting of 1,800 blood plasma samples representing 15 different types of cancer. Using liquid biopsies, 253 proteins were absolutely quantified in multiplex. The targeted method resulted in a low intra-assay variability (CV 17.2%) and a total of 1,013 peptides were quantified across almost two thousand injections. The study identified several protein targets as potential biomarker panel for the diagnosis of multiple myeloma patients using differential expression analysis and machine learning. The combination of multiple markers, including the complement complex C1, JCHAIN and CD5L, resulted in an accurate predictive model with an AUC of 0.96 for the identification of multiple myeloma patients across a cohort of various cancer patients. |
HostingRepository | PanoramaPublic |
AnnounceDate | 2024-07-03 |
AnnouncementXML | Submission_2024-07-03_19:10:30.143.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | David Kotol |
SpeciesList | scientific name: Homo sapiens; NCBI TaxID: 9606; |
ModificationList | Carbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4) |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2022-11-03 19:06:56 | ID requested | |
⏵ 1 | 2024-07-03 19:10:31 | announced |
Publication List
Kotol D, Woessmann J, Hober A, Á, lvez MB, Tran Minh KH, Pont, é, n F, Fagerberg L, Uhl, é, n M, Edfors F, Absolute Quantification of Pan-Cancer Plasma Proteomes Reveals Unique Signature in Multiple Myeloma. Cancers (Basel), 15(19):(2023) [pubmed] |
Keyword List
submitter keyword: Targeted Proteomics, Cancer, Plasma Profiling, Multiple Myeloma |
Contact List
Fredrik Edfors | |
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contact affiliation | KTH Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm, Sweden |
contact email | fredrik.edfors@scilifelab.se |
lab head | |
David Kotol | |
contact affiliation | KTH Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and Health, Stockholm, Sweden |
contact email | david.kotol@scilifelab.se |
dataset submitter |
Full Dataset Link List
Panorama Public dataset URI |