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PXD038089 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOrthogonal proteomics methods warrants development of Duchenne Muscular Dystrophy biomarkers
DescriptionBackground: Molecular components in blood, such as proteins, are used as biomarkers to detect or predict disease states, guide clinical interventions and aid in the development of therapies. While multiplexing proteomics methods promote discovery of such biomarkers, their translation to clinical use is difficult due to the lack of substantial evidence regarding their reliability as quantifiable indicators of disease state or outcome. To overcome this challenge, a novel orthogonal strategy was developed and used to assess the reliability of biomarkers and analytically corroborate already identified serum biomarkers for Duchenne muscular dystrophy (DMD). DMD is a monogenic incurable disease characterized by progressive muscle damage that currently lacks reliable and specific disease monitoring tools. Methods: Two technological platforms are used to detect and quantify the biomarkers in 72 longitudinally collected serum samples from DMD patients at 3 to 5 timepoints. Quantification of the biomarkers is achieved by detection of the same biomarker fragment either through interaction with validated antibodies in immuno-assays or through quantification of peptides by Parallel Reaction Monitoring Mass Spectrometry assay (PRM-MS). Results Five, out of ten biomarkers previously identified by affinity-based proteomics methods, were confirmed to be associated with DMD using the mass spectrometry-based method. Two biomarkers, carbonic anhydrase III and lactate dehydrogenase B, were quantified with two independent methods, sandwich immunoassays and PRM-MS, with Pearson correlations of 0.92 and 0.946 respectively. The median concentrations of CA3 and LDHB in DMD patients was elevated in comparison to those in healthy individuals by 35- and 3-fold, respectively. Levels of CA3 vary between 10.26 and 0.36 ng/ml in DMD patients whereas those of LDHB vary between 15.1 and 0.8 ng/ml. Conclusions: These results demonstrate that orthogonal assays can be used to assess the analytical reliability of biomarker quantification assays, providing a means to facilitate the translation of biomarkers to clinical practice. This strategy also warrants the development of the most relevant biomarkers, markers that can be reliably quantified with different proteomics methods.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportsupported by repository but incomplete data and/or metadata
PrimarySubmitterHelian Vunk
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListCarbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4)
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-11-10 20:02:01ID requested
12023-06-13 15:41:45announced
Publication List
Johansson C, Hunt H, Signorelli M, Edfors F, Hober A, Svensson AS, Tegel H, Forststr, ö, m B, Aartsma-Rus A, Niks E, Spitali P, Uhl, é, n M, Szigyarto CA, Orthogonal proteomics methods warrant the development of Duchenne muscular dystrophy biomarkers. Clin Proteomics, 20(1):23(2023) [pubmed]
Keyword List
submitter keyword: targeted proteomics, biomarker validation, duchenne muscular dystrophy
Contact List
Bjorn Forsstrom
contact affiliationScience for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
contact emailbjorn.forsstrom@scilifelab.se
lab head
Helian Vunk
contact affiliationScience for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
contact emailhelian.vunk@scilifelab.se
dataset submitter
Full Dataset Link List
Panorama Public dataset URI