Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6112209 | PMC |
| http://dx.doi.org/10.1155/2018/1564136 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Evaluating the Efficacy of Mebendazole Repurposing for Ovarian Cancer Therapy Using Optical Coherence Tomography.
J Biophotonics
September 2025
Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, USA.
Ovarian cancer (OvCa) remains the leading cause of gynecological cancer mortality, with most patients developing chemoresistance. Drug repurposing offers promising alternatives, with mebendazole (MBZ) showing anticancer activity. This study evaluates MBZ efficacy using Spectral Domain Optical Coherence Tomography (SD-OCT).
View Article and Find Full Text PDFBioactive compounds in 19 chili pepper varieties cultivated in Italy: Suspect screening and in vitro enzyme inhibitory effect.
Food Res Int
November 2025
Department of Food Analysis and Nutrition, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6 - Dejvice, Prague, Czech Republic.
Chili peppers have been under the spotlight of bioactivity research as they feature a diverse and rich phytochemical profile with multiple health promoting effects. These beneficial properties are related to the chemical composition of chili peppers and is of utmost importance to identify varieties with the strongest bioprospecting potential. In this study, 19 chili pepper varieties were investigated originating from Capsicum annuum L.
View Article and Find Full Text PDFStructure-guided design and triplicate molecular dynamics evaluation of mutant peptide inhibitors targeting SARS-CoV-2 main protease (Mpro).
In Silico Pharmacol
September 2025
Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S Nagar, Mohali, Punjab 160062 India.
Unlabelled: The global health crisis caused by SARS-CoV-2 underscores the urgent need for effective antiviral therapeutics. The SARS-CoV-2 main protease (Mpro) is a crucial enzyme in viral replication, making it a prime target for drug development. In this study, we designed and evaluated peptide inhibitors targeting Mpro by introducing systematic mutations in the Nsp10/11 cleavage site peptide (QLMPER).
View Article and Find Full Text PDFBeyond top-hit nontarget screening: Diagnostic fragment analysis reveals nitrogen-containing heterocycles in iron and steel industry wastewater.
J Hazard Mater
September 2025
Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China. Electronic address: wlsu
Nitrogen-containing heterocyclic compounds (NHCs), widely present in industrial wastewater, pose significant environmental and health risks, yet their identification and characterization remain poorly understood. Herein, we developed a diagnostic fragment list comprising 20 nitrogen-containing fragments for NHCs, by integrating chemical information from Pubchem with the NIST mass spectral library. Leveraging this list, we employed a diagnostic fragment-assisted nontarget screening approach and identified 151 NHCs in iron and steel industry wastewater.
View Article and Find Full Text PDFEffect-based and (non-)target chemical analyses reveal concerning levels of emerging contaminants in urban streams in Sub-Saharan Africa.
J Hazard Mater
August 2025
RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic. Electronic address:
Water contamination by micropollutants is a global issue, yet there is limited information from low-income regions. To address this, we evaluated surface water quality in rapidly growing Sub-Saharan area of Malawi lacking wastewater treatment. Integrated assessment of passive sample extracts representing wet and dry seasons combined effect-based approach with in vitro bioassays, target and non-target chemical analyses (NTS).
View Article and Find Full Text PDF