Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants
AbstractMolecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics ma...
Source: Clinical Proteomics - August 12, 2021 Category: Biochemistry Source Type: research
Proteome profiling of human placenta reveals developmental stage-dependent alterations in protein signature
ConclusionAccording to Reactome and PANTHER softwares, these proteins were mostly involved in response to chemical stimulus and stress, regulation of biological quality, programmed cell death, hemostatic and catabolic processes, protein folding, cellular oxidant detoxification, coagulation and retina homeostasis. Elucidation of alteration in protein signature during placental development would provide researchers with a better understanding of the critical biological processes of placentogenesis and delineate proteins involved in regulation of placental function during development. (Source: Clinical Proteomics)
Source: Clinical Proteomics - August 9, 2021 Category: Biochemistry Source Type: research
The plasma peptides of Alzheimer ’s disease
ConclusionProteins apparently expressed in the brain that were directly related to Alzheimer ’s including Nerve Growth Factor (NFG), Sphingomyelin Phosphodiesterase, Disrupted in Schizophrenia 1 (DISC1), the cell death regulator retinitis pigmentosa (NXNl1) that governs the loss of nerve cells in the retina and the cell death regulator ZC3H12A showed much higher observation frequency in A D plasma vs the matched control. There was a striking agreement between the proteins known to be mutated or dis-regulated in the brains of AD patients with the proteins observed in the plasma of AD patients from endogenous peptides incl...
Source: Clinical Proteomics - June 28, 2021 Category: Biochemistry Source Type: research
Quantitative proteomic analysis of aberrant expressed lysine acetylation in gastrointestinal stromal tumors
ConclusionsOur novel findings provide further understanding of acetylome in GIST and might demonstrate the possibility in the acetylation targeted diagnosis and therapy of GIST. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 22, 2021 Category: Biochemistry Source Type: research
A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)
ConclusionWe propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays. (Source: Clinical Proteomics)
Source: Clinical Proteomics - May 10, 2021 Category: Biochemistry Source Type: research
O-GlcNAcylation protein disruption by Thiamet G promotes changes on the GBM U87-MG cells secretome molecular signature
AbstractGlioblastoma (GBM) is a grade IV glioma highly aggressive and refractory to the therapeutic approaches currently in use. O-GlcNAcylation plays a key role for tumor aggressiveness and progression in different types of cancer; however, experimental evidence of its involvement in GBM are still lacking. Here, we show that O-GlcNAcylation plays a critical role in maintaining the composition of the GBM secretome, whereas inhibition of OGA activity disrupts the intercellular signaling via microvesicles. Using a label-free quantitative proteomics methodology, we identified 51 proteins in the GBM secretome whose abundance w...
Source: Clinical Proteomics - April 26, 2021 Category: Biochemistry Source Type: research
The use of proteomics for blood biomarker research in premature infants: a scoping review
The objective of this scoping review was to identify the existing literature, as well as any knowledge gaps related to proteomic biomarker discoveries in the setting of prematurity. A scoping review was conducted using PubMed, Embase and Medline databases following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines. The study selection process yielded a total of 700 records, of which 13 studies were included in this review. Most studies used a tandem Mass Spectrometry (MS/MS) proteomics approach to identify key biomarkers. The corresponding studies i...
Source: Clinical Proteomics - April 14, 2021 Category: Biochemistry Source Type: research
The associations between red cell distribution width and plasma proteins in a general population
ConclusionsSeveral proteins from this targeted proteomics panel were associated with RDW in this cohort. These proteins could potentially be linked to the increased cardiovascular risk in individuals with high RDW. (Source: Clinical Proteomics)
Source: Clinical Proteomics - March 30, 2021 Category: Biochemistry Source Type: research
Circulating proteins associated with allergy development in infants —an exploratory analysis
ConclusionSampled at one month of age, circulating proteins that reflect processes of the immune system may predict the development of allergic disease later in childhood. (Source: Clinical Proteomics)
Source: Clinical Proteomics - March 15, 2021 Category: Biochemistry Source Type: research
Rational selection of a biomarker panel targeting unmet clinical needs in kidney injury
AbstractThe pipeline of biomarker translation from bench to bedside is challenging and limited biomarkers have been adopted to routine clinical care. Ideally, biomarker research and development should be driven by unmet clinical needs in health care. To guide researchers, clinical chemists and clinicians in their biomarker research, the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) has developed a structured questionnaire in which the clinical gaps in current clinical pathways are identified and desirable performance specifications are predefined. In kidney injury, the high prevalence of the synd...
Source: Clinical Proteomics - February 22, 2021 Category: Biochemistry Source Type: research
Proteomic analysis of decidua in patients with recurrent pregnancy loss (RPL) reveals mitochondrial oxidative stress dysfunction
ConclusionsThis comprehensive analysis of RPL proteomics reveals novel candidate: NDUFB3, which could be further investigated for explanation of the pathological mechanism of RPL. (Source: Clinical Proteomics)
Source: Clinical Proteomics - February 22, 2021 Category: Biochemistry Source Type: research
Time dependent effect of cold ischemia on the phosphoproteome and protein kinase activity in fresh-frozen colorectal cancer tissue obtained from patients
ConclusionsThe vast majority of the phosphoproteome as well as the activity of protein kinases in colorectal cancer resection tissue is stable up to 180 min of CIT and reflects tumor characteristics. However, specific changes in kinase activity with increasing CIT were observed. Therefore, stringent tissue collection procedures are advised to minimize changes in kinase activity during CIT. (Source: Clinical Proteomics)
Source: Clinical Proteomics - February 18, 2021 Category: Biochemistry Source Type: research
Quantitative proteomics analysis of lysine 2-hydroxyisobutyrylation in IgA nephropathy
ConclusionsImportantly, the abundance of lipocalin 2 was increased in the differentially expressed proteins, and a KEGG-based functional enrichment analysis showed that Khib proteins clustered in the IL-17 signaling pathway and phagosome category, which may have important associations with IgAN. Our data enlighten our understanding of Khib in IgAN and indicate that Khib may have important regulatory roles in IgAN. (Source: Clinical Proteomics)
Source: Clinical Proteomics - February 8, 2021 Category: Biochemistry Source Type: research
Quantitative proteomics-based analyses performed on pre-eclampsia samples in the 2004 –2020 period: a systematic review
AbstractBackgroundQuantitative proteomics is an invaluable tool in biomedicine for the massive comparative analysis of protein component of complex biological samples. In the last two decades, this technique has been used to describe proteins potentially involved in the pathophysiological mechanisms of preeclampsia as well as to identify protein biomarkers that could be used with diagnostic/prognostic purposes in pre-eclampsia.ResultsWe have done a systematic review of all proteomics-based papers describing differentially expressed proteins in this disease. Searching Pubmed with the terms pre-eclampsia and proteomics, rest...
Source: Clinical Proteomics - January 26, 2021 Category: Biochemistry Source Type: research
Variable blood processing procedures contribute to plasma proteomic variability
ConclusionsVariable blood processing procedures contribute significantly to plasma proteomic variation and may give rise to increased intracellular proteins in plasma. Accounting for these effects can be important both at study design and data analysis stages. This understanding will be valuable to incorporate in the planning of protein-based biomarker discovery efforts in the future. (Source: Clinical Proteomics)
Source: Clinical Proteomics - January 19, 2021 Category: Biochemistry Source Type: research
