sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides
ConclusionsDetection of biotinylation sites on cell surface proteins using sBioSITe provides a reliable method for identifying cell surface proteins. This strategy complements existing methods for detection of cell surface expressed proteins especially in discovery-based proteomics approaches. (Source: Clinical Proteomics)
Source: Clinical Proteomics - December 5, 2023 Category: Biochemistry Source Type: research
Quantitative proteomics analysis based on data-independent acquisition reveals the effect of Shenling Baizhu powder (SLP) on protein expression in MAFLD rat liver tissue
ConclusionSLP ameliorates hepatic steatosis to exert therapeutic effects on MAFLD by inhibiting the expression of lipid synthesis genes and inhibiting lipid peroxidation in mitochondria. This study provides a new idea and basis for the study of SLP in the treatment of MAFLD and provides an experimental basis for the clinical application of SLP. (Source: Clinical Proteomics)
Source: Clinical Proteomics - December 1, 2023 Category: Biochemistry Source Type: research
Validation of the novel GLAS algorithm as an aid in the detection of liver fibrosis and cirrhosis based on GP73, LG2m, age, and sex
ConclusionsGP73 and LG2m serum biomarkers, when combined with age and sex (GLAS algorithm), showed high sensitivity and specificity for detection of liver disease in two independent cohorts. The GLAS algorithm will need to be validated and refined in larger cohorts and tested in longitudinal studies for differentiating between stable versus advancing liver disease over time. (Source: Clinical Proteomics)
Source: Clinical Proteomics - November 28, 2023 Category: Biochemistry Source Type: research
Proteomic analysis of chromophobe renal cell carcinoma and benign renal oncocytoma biopsies reveals shared metabolic dysregulation
ConclusionsThis study underscores the value of integrating high-resolution mass spectrometry protein quantification to effectively characterize and differentiate the proteomic landscapes of solid tumor biopsies diagnosed as chRCC and RO. The insights gained from this research offer valuable information for enhancing our understanding of these conditions and may aid in the development of improved diagnostic and therapeutic strategies. (Source: Clinical Proteomics)
Source: Clinical Proteomics - November 28, 2023 Category: Biochemistry Source Type: research
Development of a predictive model to distinguish prostate cancer from benign prostatic hyperplasia by integrating serum glycoproteomics and clinical variables
ConclusionsTo address the impelling need of more sensitive and specific serum diagnostic tests, a predictive model combining proteomic and clinical variables was developed. A preliminary evaluation to build a new tool able to discriminate aggressive presentations of PCa from tumors with benign behavior was exploited. This predictor displayed moderate performances, but no conclusions can be drawn due to the limited number of the sample cohort.Data are available via ProteomeXchange with identifier PXD035935. (Source: Clinical Proteomics)
Source: Clinical Proteomics - November 21, 2023 Category: Biochemistry Source Type: research
Comparison of in-gel and in-solution proteolysis in the proteome profiling of organ perfusion solutions
ConclusionsThis study showed that in-solution digestion is a more efficient method for LC-MS/MS analysis of kidney and liver organ perfusion solutions. This method is also quicker and easier than in-gel digestion, allowing for greater sample throughput, with fewer opportunities for experimental error or peptide loss. (Source: Clinical Proteomics)
Source: Clinical Proteomics - November 15, 2023 Category: Biochemistry Source Type: research
A pathway activity-based proteomic classifier stratifies prostate tumors into two subtypes
AbstractProstate cancer (PCa) is the second most common cancer in males worldwide. The risk stratification of PCa is mainly based on morphological examination. Here we analyzed the proteome of 667 tumor samples from 487 Chinese PCa patients and characterized 9576 protein groups by PulseDIA mass spectrometry. Then we developed a pathway activity-based classifier concerning 13 proteins from seven pathways, and dichotomized the PCa patients into two subtypes, namely PPS1 and PPS2. PPS1 is featured with enhanced innate immunity, while PPS2 with suppressed innate immunity. This classifier exhibited a correlation with PCa progre...
Source: Clinical Proteomics - November 11, 2023 Category: Biochemistry Source Type: research
Candidate biomarkers for treatment benefit from sunitinib in patients with advanced renal cell carcinoma using mass spectrometry-based (phospho)proteomics
In conclusion, the RCC (phospho)proteome revealed differentialp-sites and kinase activities associated with sunitinib resistance and sensitivity. Independent validation is warranted to develop an assay for upfront identification of patients who are intrinsically resistant to sunitinib. (Source: Clinical Proteomics)
Source: Clinical Proteomics - November 8, 2023 Category: Biochemistry Source Type: research
Mass spectrometry quantifies target engagement for a KRASG12C inhibitor in FFPE tumor tissue
ConclusionsThis work illustrates the potential to expand mass spectrometry-based proteomics in preclinical and clinical oncology drug development through analysis of FFPE tumor biopsies. (Source: Clinical Proteomics)
Source: Clinical Proteomics - October 25, 2023 Category: Biochemistry Source Type: research
Change of histone H3 lysine 14 acetylation stoichiometry in human monocyte derived macrophages as determined by MS-based absolute targeted quantitative proteomic approach: HIV infection and methamphetamine exposure
ConclusionsThe developed LC –MS/MS assay enabled absolute quantification of H3K14Ac in exposed to Meth HIV-infected hMDM. It can be further applied determination of this PTM stoichiometry in other studies on human primary macrophages.Graphical Abstract (Source: Clinical Proteomics)
Source: Clinical Proteomics - October 25, 2023 Category: Biochemistry Source Type: research
Comment on “Cerebrospinal fluid camk2a levels at baseline predict long-term progression in multiple sclerosis. Clinical Proteomics”
(Source: Clinical Proteomics)
Source: Clinical Proteomics - October 25, 2023 Category: Biochemistry Source Type: research
Glial cell proteome using targeted quantitative methods for potential multi-diagnostic biomarkers
In this study, five proteins (CCT3, PCMT1, TKT, TOMM34, UBA1) showed the significantly different protein levels (t-test: p value ≤ 0.05, AUC ≥ 0.7) between control and cancer groups and the result of multiplex assay using logistic re gression showed the 5-marker panel showed better sensitivity (0.80 and 0.90), specificity (0.92 and 1.00), error rate (10 and 2%), and AUC value (0.94 and 0.98) than the best single marker (TOMM34) in primary cells and tissues, respectively. Although we acknowledge that the model requires further va lidation in a large sample size, the 5 protein marker panel can be used as baseline...
Source: Clinical Proteomics - October 24, 2023 Category: Biochemistry Source Type: research
Validation of ANG-1 and P-SEL as biomarkers of post-COVID-19 conditions using data from the Biobanque qu ébécoise de la COVID-19 (BQC-19)
AbstractThe quest for understanding and managing the long-term effects of COVID-19, often referred to as Long COVID or post-COVID-19 condition (PCC), remains an active research area. Recent findings highlighted angiopoietin-1 (ANG-1) and p-selectin (P-SEL) as potential diagnostic markers, but validation is essential, given the inconsistency in COVID-19 biomarker studies. Leveraging the biobanque qu ébécoise de la COVID-19 (BQC19) biobank, we analyzed the data of 249 participants. Both ANG-1 and P-SEL levels were significantly higher in patients with PCC participants compared with control subjects at 3 months using the Ma...
Source: Clinical Proteomics - October 24, 2023 Category: Biochemistry Source Type: research
Proteomic analyses reveal cystatin c is a promising biomarker for evaluation of systemic lupus erythematosus
ConclusionsNeutrophil activation is more prominent in SLE with proteinuria and anti-dsDNA positivity, and CysC is a promising marker for monitoring organ damage and disease activity in SLE. (Source: Clinical Proteomics)
Source: Clinical Proteomics - October 18, 2023 Category: Biochemistry Source Type: research
Redefining serological diagnostics with immunoaffinity proteomics
AbstractSerological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The advantages of straightforward setup and manufacturing, analytical sensitivity and specificity, affordability, and high-throughput measurements were accompanied by limitations such as semi-quantitative measurements, lac...
Source: Clinical Proteomics - October 12, 2023 Category: Biochemistry Source Type: research
