Correction: Glial cell proteome using targeted quantitative methods for potential multi-diagnostic biomarkers
(Source: Clinical Proteomics)
Source: Clinical Proteomics - February 10, 2024 Category: Biochemistry Source Type: research

Absolute quantitation of human wild-type DNAI1 protein in lung tissue using a nanoLC-PRM-MS-based targeted proteomics approach coupled with immunoprecipitation
ConclusionsThe results clearly demonstrate that the developed assay can accurately quantitate low-abundance WT DNAI1 protein in human lung tissue with high sensitivity, indicating its high potential use in the drug development for DNAI1 mutation-caused PCD therapy. (Source: Clinical Proteomics)
Source: Clinical Proteomics - February 4, 2024 Category: Biochemistry Source Type: research

Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma
ConclusionsOur study demonstrates the feasibility of multi-omics data generation from tissue cores, the necessity of interval H&E stains in serial histology sections, and the utility of coring to improve analysis over bulk tissue data. (Source: Clinical Proteomics)
Source: Clinical Proteomics - January 30, 2024 Category: Biochemistry Source Type: research

Recent developments in mass-spectrometry-based targeted proteomics of clinical cancer biomarkers
AbstractRoutine measurement of cancer biomarkers is performed for early detection, risk classification, and treatment monitoring, among other applications, and has substantially contributed to better clinical outcomes for patients. However, there remains an unmet need for clinically validated assays of cancer protein biomarkers. Protein tumor markers are of particular interest since proteins carry out the majority of biological processes and thus dynamically reflect changes in cancer pathophysiology. Mass spectrometry-based targeted proteomics is a powerful tool for absolute peptide and protein quantification in biological...
Source: Clinical Proteomics - January 30, 2024 Category: Biochemistry Source Type: research

An LC –MS-based designated comparison method with similar performance to the Lp(a) reference measurement procedure to guide molar Lp(a) standardization
ConclusionsThe semi-automated, higher throughput, LC –MS-based method for Lp(a) meets the predefined analytical performance specifications and allowable MU and is hence applicable as a higher order Designated Comparison Method, which is ideally suited to guide IVD manufacturers in the transition from Lp(a) mass to molar units. (Source: Clinical Proteomics)
Source: Clinical Proteomics - January 24, 2024 Category: Biochemistry Source Type: research

Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling
ConclusionsHere we identified extensive three-dimensional heterogeneity within the USC tumor microenvironment, with disease-relevant biomarkers present in both the tumor and the stroma. These data underscore the critical need for upfront enrichment of cellular subpopulations from tissue specimens for spatial proteogenomic analysis. (Source: Clinical Proteomics)
Source: Clinical Proteomics - January 22, 2024 Category: Biochemistry Source Type: research

Kinase inhibitor pulldown assay (KiP) for clinical proteomics
AbstractProtein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with ...
Source: Clinical Proteomics - January 16, 2024 Category: Biochemistry Source Type: research

Prognostic biomarker discovery based on proteome landscape of Chinese lung adenocarcinoma
This study provided insights for improved understanding proteome abnormalities of LUAD and the novel prognostic biomarker discovery offered an opportunity for LUAD precise management. (Source: Clinical Proteomics)
Source: Clinical Proteomics - January 5, 2024 Category: Biochemistry Source Type: research

Quantification of putative ovarian cancer serum protein biomarkers using a multiplexed targeted mass spectrometry assay
ConclusionsA multiplexed targeted PRM MS assay was applied to detect candidate diagnostic biomarkers in HGSOC sera. To evaluate the clinical utility of the IBP2 PRM assay for HGSOC detection, further studies need to be performed using a larger patient cohort. (Source: Clinical Proteomics)
Source: Clinical Proteomics - January 3, 2024 Category: Biochemistry Source Type: research

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