Alzheimer's disease (AD) lacks protein biomarkers reflective of its diverse underlying pathophysiology, hindering diagnostic and therapeutic advancements. Here, we used integrative proteomics to identify cerebrospinal fluid (CSF) biomarkers representing a wide spectrum of AD pathophysiology. Multiplex mass spectrometry identified ~3500 and ~12,000 proteins in AD CSF and brain, respectively. Network ... More
METTL16 inhibits pancreatic cancer proliferation and metastasis by promoting MROH8 RNA stability and inhibiting CAPN2 expression - experimental studies.
JournalInternational journal of surgery (London, England)
PubMed ID39434688
BACKGROUND: N6-methyladenosine (m6A) modification plays a crucial role in the progression of various cancers, including pancreatic cancer, by regulating gene expression. However, the specific mechanisms by which m6A affects pancreatic cancer metastasis remain unclear. This study aims to elucidate the role of METTL16, an m6A writer gene, in regulating core ... More
Proteomic profiling identifies SPP1 associated with rapidly progressive interstitial lung disease in anti-MDA5-positive dermatomyositis.
BACKGROUND: Anti-melanoma differentiation-associated gene five antibody positive (MDA5(+)) dermatomyositis (DM) is significantly associated with rapidly progressive interstitial lung disease (RP-ILD). Early detection of RP-ILD remains a major challenge. This study aims to identify and validate prognostic factors for RP-ILD in MDA5(+) DM patients. METHODS: Plasma samples from 20 MDA5(+) DM ... More
Enhancing Proteomics Quality Control: Insights from the Visualization Tool QCeltis.
Large-scale mass-spectrometry-based proteomics experiments are complex and prone to analytical variability, requiring rigorous quality checks across each step in the workflow: sample preparation, chromatography, mass spectrometry, and the bioinformatics stages. This includes quality control (QC) measures that address biological and technical variation. Most QC approaches involve detecting sample outliers and ... More
Tandem mass tag-based quantitative proteomic profiling identifies candidate serum biomarkers of drug-induced liver injury in humans.
Diagnosis of drug-induced liver injury (DILI) and its distinction from other liver diseases are significant challenges in drug development and clinical practice. Here, we identify, confirm, and replicate the biomarker performance characteristics of candidate proteins in patients with DILI at onset (DO; n = 133) and follow-up (n = 120), acute non-DILI at onset ... More
Design of experiments approach for systematic optimization of a single-shot diaPASEF plasma proteomics workflow applicable for high-throughput.
AuthorsRice SJ,Belani CP
JournalProteomics. Clinical applications
PubMed ID37650339
PURPOSE: Plasma is an abundant source of protein biomarkers. Mass spectrometry (MS) is an effective means to measure a large number of proteins in a single run. The recent development of data-independent acquisition with parallel accumulation and serial fragmentation (diaPASEF) on a trapped ion mobility spectrometer (TIMS) affords deep proteomic ... More
A proteomic classifier panel for early screening of colorectal cancer: a case control study.
BACKGROUND: Diagnosis of colorectal cancer (CRC) during early stages can greatly improve patient outcome. Although technical advances in the field of genomics and proteomics have identified a number of candidate biomarkers for non-invasive screening and diagnosis, developing more sensitive and specific methods with improved cost-effectiveness and patient compliance has tremendous ... More
Diagnostic signatures and immune cell infiltration characteristics in anti-GABA(B)R encephalitis.
PURPOSE: Anti-gamma-aminobutyric acid B receptor (GABA(B)R) encephalitis is an uncommon form of autoimmune encephalitis associated with a poor prognosis and a high fatality rate. We aim to find diagnostic markers for anti- GABA(B)R encephalitis as well as the effects of immune cell infiltration on this pathology. METHODS: For quantitative proteomic ... More