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Absolute Quantification of Pan-Cancer Plasma Proteomes Reveals Unique Signature in Multiple Myeloma
KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-5388-3826
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.ORCID iD: 0000-0002-2283-7237
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.ORCID iD: 0000-0001-8947-2562
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.ORCID iD: 0000-0002-2669-7796
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2023 (English)In: Cancers, ISSN 2072-6694, Vol. 15, no 19, article id 4764Article in journal (Refereed) Published
Abstract [en]

Mass spectrometry based on data-independent acquisition (DIA) has developed into a powerful quantitative tool with a variety of implications, including precision medicine. Combined with stable isotope recombinant protein standards, this strategy provides confident protein identification and precise quantification on an absolute scale. Here, we describe a comprehensive targeted proteomics approach to profile a pan-cancer cohort consisting of 1800 blood plasma samples representing 15 different cancer types. We successfully performed an absolute quantification of 253 proteins in multiplex. The assay had low intra-assay variability with a coefficient of variation below 20% (CV = 17.2%) for a total of 1013 peptides quantified across almost two thousand injections. This study identified a potential biomarker panel of seven protein targets for the diagnosis of multiple myeloma patients using differential expression analysis and machine learning. The combination of markers, including the complement C1 complex, JCHAIN, and CD5L, resulted in a prediction model with an AUC of 0.96 for the identification of multiple myeloma patients across various cancer patients. All these proteins are known to interact with immunoglobulins.

Place, publisher, year, edition, pages
MDPI AG , 2023. Vol. 15, no 19, article id 4764
Keywords [en]
DIA, multiple myeloma, precision medicine, targeted proteomics
National Category
Cancer and Oncology Hematology
Identifiers
URN: urn:nbn:se:kth:diva-338876DOI: 10.3390/cancers15194764ISI: 001086709700001PubMedID: 37835457Scopus ID: 2-s2.0-85173822408OAI: oai:DiVA.org:kth-338876DiVA, id: diva2:1808429
Note

QC 20231115

Available from: 2023-10-31 Created: 2023-10-31 Last updated: 2023-12-07Bibliographically approved

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Kotol, DavidWoessmann, JakobHober, AndreasAlvez, Maria BuenoFagerberg, LinnUhlén, MathiasEdfors, Fredrik

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Kotol, DavidWoessmann, JakobHober, AndreasAlvez, Maria BuenoTran Minh, Khue HuaFagerberg, LinnUhlén, MathiasEdfors, Fredrik
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Systems BiologyScience for Life Laboratory, SciLifeLab
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