Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

Ignjatović, Vera; Geyer, Philipp; Palaniappan, Krishnan K.; Chaaban, Jessica E.; Omenn, Gilbert S.; Baker, Mark S.; Deutsch, Eric W.; Schwenk, Jochen M.

doi:10.1021/acs.jproteome.9b00503

Cited by 159 publications

(156 citation statements)

References 152 publications

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“…In this sense, MS-based proteome analysis of plasma and serum is unbiased and in principle an ideal technology for systems-wide characterization of disease response (Geyer et al ., 2017). In practice, body fluid proteomics is very challenging but continuous technological improvements have led to a resurgence of interest (Geyer et al ., 2017; Ignjatovic et al ., 2019; Suhre, McCarthy and Schwenk, 2021).…”

Section: Introductionmentioning

confidence: 99%

High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion

Geyer

Arend

Doll

et al. 2021

Preprint

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Biomarkers for COVID-19 are urgently needed. Here we bring the powerful technology of mass spectrometry (MS)-based proteomics to bear on this challenge. We measured serum proteomes of COVID-19 patients and symptomatic, but PCR-negative controls, in a time-resolved manner. In 262 controls and 458 longitudinal samples (average of 31 days) of 31 patients, hospitalized for COVID-19, a remarkable 26% of proteins changed significantly. Bioinformatics analyses revealed co-regulated groups and shared biological functions. Proteins of the innate immune system such as CRP, SAA1, CD14, LBP and LGALS3BP decreased early in the time course. In contrast, regulators of coagulation (APOH, FN1, HRG, KNG1, PLG) and lipid homeostasis (APOA1, APOC1, APOC2, APOC3, PON1) increased over the course of the disease. A global correlation map provides a systems-wide functional association between proteins, biological processes and clinical chemistry parameters. Importantly, five SARS-CoV-2 immunoassays against antibodies revealed excellent correlations with an extensive range of immunoglobulin regions, which were quantified by MS-based proteomics. The high-resolution profile of all immunoglobulin regions showed individual-specific differences and commonalities of potential pathophysiological relevance.

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Section: Introductionmentioning

confidence: 99%

High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion

Geyer

Arend

Doll

et al. 2021

Preprint

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“…The blood proteome, consisting of both cellular and soluble proteins, has received a revived interest due to advances in protein technologies. This includes mass cytometry [5] to study immune systems, as well as mass spectrometry [6] and affinity assays [7] for profiling serum or plasma. For the circulating plasma proteome, nearly 5,000 proteins have this far been detected when combing discoveries from all assays and technologies [8].…”

Section: Introductionmentioning

confidence: 99%

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

Dodig‐Crnković

Hong

Thomas

et al. 2020

Preprint

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Background: Precision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate.Methods: To provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals' short-term health trajectories. Findings:We found signatures of circulating proteomes to be highly individualspecific. Considering technical and longitudinal variability, we observed both stable and fluctuating proteins in the circulation, as well as networks of proteins that covaried over time. For each participant, there were unique protein profiles and some of these could be explained by associations to genetic variants.Interpretation: This study demonstrates that there was noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. Longitudinal profiling of circulating proteomes has the potential to enable a more personal hence precise assessment of health states, and thereby provide a valuable component of precision medicine approaches.

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“…Proteomics, defined as the systematic analysis of proteins expressed by an organism at a given time, under certain conditions, has become a powerful tool in bioscience to identify new disease-specific proteins [8][9][10][11]. Several proteomic studies have been successfully performed for different painful condition, e.g., rheumatoid arthritis, neuropathic pain, fibromyalgia, burning mouth syndrome, and trapezius myalgia by analyzing proteins in saliva, plasma, synovial fluid, interstitial fluid, or biopsies [12][13][14][15][16][17][18][19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Protein Signature in Saliva of Temporomandibular Disorders Myalgia

Jasim

Ernberg

Carlsson

et al. 2020

IJMS

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In the last years, several attempts have been made to study specific biological markers of temporomandibular disorders (TMD). So far, no laboratory tests have been appropriately validated for the diagnosis and prognosis of these disorders. This study aimed to investigate the proteomic profile of the whole stimulated saliva of TMD myalgia patients in order to evaluate potential diagnostic and/or prognostic salivary candidate proteins which could be useful for the management of TMD. Twenty patients diagnosed with TMD myalgia according to the validated Diagnostic Criteria for TMD (DC/TMD) and 20 matched healthy pain-free controls were enrolled. Saliva samples were collected in the morning. Comparative proteomic analysis was performed with two-dimensional gel electrophoresis followed by identification with liquid chromatography-tandem mass spectrometry. Statistical analysis of the quantitative proteomics data revealed that 20 proteins were significantly altered in patients compared to controls. Among these proteins, 12 showed significantly increased levels, and 8 showed significantly decreased levels in patients with TMD myalgia compared to controls. The identified proteins are involved in metabolic processes, immune response, and stress response. This proteomic study shows that the salivary protein profile can discriminate patients with TMD myalgia from healthy subjects, but the protein signature has no correlation with the clinical features of TMD myalgia. Additional studies are needed to validate our observations in additional sample sets and to continue assessing the utility of saliva as a suitable sample for studying processes related to TMD myalgia.

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Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

Cited by 159 publications

References 152 publications

High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion

High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

Protein Signature in Saliva of Temporomandibular Disorders Myalgia

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