Advances in mass spectrometry-based clinical biomarker discovery

Crutchfield, Christopher A.; Thomas, Stefani N.; Sokoll, Lori J.; Chan, Daniel W.

doi:10.1186/s12014-015-9102-9

Cited by 234 publications

(167 citation statements)

References 77 publications

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“…They differ markedly by the ionization source of the sample. The main sources used in proteomic analysis are matrix-assisted laser desorption/ionization (MALDI) and surface-enhancer laser desorption/ionization (SELDI) [10,11]. These techniques allow a soft ionization of molecules without excessive fragmentation [9,11].…”

Section: (Iv)mentioning

confidence: 99%

Chondrocyte secretome: a source of novel insights and exploratory biomarkers of osteoarthritis

Sanchez

Bay‐Jensen

Pap

et al. 2017

Osteoarthritis and Cartilage

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The extracellular matrix (ECM) of articular cartilage is comprised of complex networks of proteins and glycoproteins, all of which are expressed by its resident cell, the chondrocyte. Cartilage is a unique tissue given its complexity and ability to resist repeated load and deformation. The mechanisms by which articular cartilage maintains its integrity throughout our lifetime is not fully understood, however there are numerous regulatory pathways known to govern ECM turnover in response to mechanical stimuli. To further our understanding of this field, we envision that proteomic analysis of the secretome will provide information on how the chondrocyte remodels the surrounding ECM in response to load, in addition to providing information on the metabolic state of the cell. In this review, we attempt to summarize the recent mass spectrometry-based proteomic discoveries in healthy and diseased cartilage and chondrocytes, to facilitate the discovery of novel biomarkers linked to degenerative pathologies, such as osteoarthritis (OA).

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Section: (Iv)mentioning

confidence: 99%

Chondrocyte secretome: a source of novel insights and exploratory biomarkers of osteoarthritis

Sanchez

Bay‐Jensen

Pap

et al. 2017

Osteoarthritis and Cartilage

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“…With MS, ambiguous quantifications are eliminated, especially when tandem MS (MS/MS) is used. Recently, high-resolution instruments such as the linear ion trap Orbitrap, the quadrupole-TOF (Q-TOF), and the Triple-TOF analyzers are commonly used in biomarker discovery studies and ideal for top-down proteomics [26,27]. …”

Section: Blood Omicsmentioning

confidence: 99%

The search for drug-targetable diagnostic, prognostic and predictive biomarkers in chronic graft-versus-host disease

Ren

Adom

Paczesny

2018

Expert Review of Clinical Immunology

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Introduction Chronic graft-versus-host disease (cGVHD) continues to be the leading cause of late morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT), which is an increasingly applied curative method for both benign and malignant hematologic disorders. Biomarker identification is crucial for the development of noninvasive and cost-effective cGVHD diagnostic, prognostic, and predictive test for use in clinic. Furthermore, biomarkers may help to gain a better insight on ongoing pathophysiological processes. The recent widespread application of omics technologies including genomics, transcriptomics, proteomics and cytomics provided opportunities to discover novel biomarkers. Areas covered This review focuses on biomarkers identified through omics that play a critical role in target identification for drug development, and that were verified in at least two independent cohorts. It also summarizes the current status on omics tools used to identify these useful cGVHD targets. We briefly list the biomarkers identified and verified so far. We further address challenges associated to their exploitation and application in the management of cGVHD patients. Finally, insights on biomarkers that are drug targetable and represent potential therapeutic targets are discussed. Expert commentary We focus on biomarkers that play an essential role in target identification.

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“…Since MALDI-TOF MS is, in principle, able to identify any ionizable compound [61], it can detect antibiotic resistance (e.g., via the identification of specific proteins or degradation products of antibiotics), but has also been used to reveal recombinant proteins, plasmid insertions in bacteria, or other biomarkers and diagnostic peptides in bacteria [62][63][64][65][66].…”

Section: Maldi-tof Ms Applications Beyond Species Identificationmentioning

confidence: 99%

MALDI-TOF mass spectroscopy of yeasts and filamentous fungi for research and diagnostics in the agricultural value chain

Drissner

Freimoser

2017

Chem. Biol. Technol. Agric.

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Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS; MALDI biotyping) has become a standard tool for the accurate, rapid, and economical identification of pathogens in the clinical diagnostics laboratory. The method is continuously being improved, and new applications for distinguishing strains, identifying metabolites or functional characteristics (e.g., antibiotic resistance), and detecting microbes directly in patient samples have been developed. Adopting these methods in other disciplines than clinical diagnostics, for example, in agriculture, food safety and quality testing, or ecology, will open up new opportunities for diagnostics and research. This review focuses on MALDI-TOF MS approaches for the identification of yeasts and filamentous fungi. In contrast to bacterial diagnostics, MALDI biotyping of fungi is more challenging and less established. We thus start by discussing the role of MALDI-TOF MS as a tool for species identification; in particular with respect to DNA-based identification methods. The review then highlights the value of custom-made reference spectra for MALDI biotyping and points out recent advancements of MALDI-TOF MS, mainly from the field of clinical diagnostics that may be adopted and used for fungal diagnostic challenges. The overview ends with a summary of MALDI-TOF MS studies of yeasts and filamentous fungi of agricultural relevance.

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Advances in mass spectrometry-based clinical biomarker discovery

Cited by 234 publications

References 77 publications

Chondrocyte secretome: a source of novel insights and exploratory biomarkers of osteoarthritis

Chondrocyte secretome: a source of novel insights and exploratory biomarkers of osteoarthritis

The search for drug-targetable diagnostic, prognostic and predictive biomarkers in chronic graft-versus-host disease

MALDI-TOF mass spectroscopy of yeasts and filamentous fungi for research and diagnostics in the agricultural value chain

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