A5090908007- Glycosylation and Glycoproteins Research
- Advanced Proteomics Techniques and Applications
- Genomics and Phylogenetic Studies
- Carbohydrate Chemistry and Synthesis
- Machine Learning in Bioinformatics
- Monoclonal and Polyclonal Antibodies Research
- Photoreceptor and optogenetics research
- Luminescence and Fluorescent Materials
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Sensors and Ion Detection
- Proteoglycans and glycosaminoglycans research
- Mass Spectrometry Techniques and Applications
- Peptidase Inhibition and Analysis
HUN-REN Szegedi Biológiai Kutatóközpont
2016-2022
University of Szeged
2018-2022
Hungarian Research Network
2022
Michigan Technological University
2018
Houghton University
2018
Hungarian Academy of Sciences
2016-2018
Abstract Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through HUPO Human Initiative, this community study, comprising both developers and users glycoproteomics software, evaluates solutions for system-wide analysis. The same spectrometry based datasets from human serum were shared with participants team...
New near-infrared rhodamine dyes with large Stokes shifts were developed and applied for sensitive detection of cellular pH changes fluctuations by incorporating an additional amine group fused rings.
A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest urinary proteins three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic Protein Prospector, were used for interpretation data, O-linked glycopeptides assigned separate searches. The identification rate low in all searches, even when results combined. Thus, we investigated...
A relatively novel activation technique, electron-transfer/higher-energy collision dissociation (EThcD) was used in the LC-MS/MS analysis of tryptic glycopeptides enriched with wheat germ agglutinin from human urine samples. We focused on characterization mucin-type O-glycopeptides. EThcD a single spectrum provided information both peptide modified and glycan carried. Unexpectedly, oxonium ions indicated presence O-acetyl, even O-diacetyl-sialic acids. B Y fragment revealed that (i) core 1...
Intact glycopeptide analysis is becoming more common with developments in mass spectrometry instrumentation and fragmentation approaches. In particular, collision-based approaches such as higher energy collisional dissociation (HCD) radical-driven electron transfer (ETD) provide complementary information, but bioinformatic strategies to utilize this combined information are currently lacking. work we adapted a software tool, MS-Filter, search HCD peak list files for predicted Y ions based on...
Glycopeptides represent cross-linked structures between chemically and physically different biomolecules. Mass spectrometric analysis of O-glycopeptides may reveal the identity peptide, composition glycan even connection certain sugar units, but usually only combination MS/MS techniques provides sufficient information for reliable assignment. Currently, HCD followed by diagnostic fragment-triggered ETD or EThcD experiments is most promising data acquisition protocol. However, content handled...
While N-glycopeptides are relatively easy to characterize, O-glycosylation analysis is more complex. In this article, we illustrate the multiple layers of O-glycopeptide characterization that make task so challenging. We believe our carefully curated dataset represents perhaps largest intact human glycopeptide mixture derived from individuals, not cell lines. The samples were collected healthy patients with superficial or advanced bladder cancer (three each group), and a single inflammation...
Abstract Glycoproteome profiling (glycoproteomics) is a powerful yet analytically challenging research tool. The complex tandem mass spectra generated from glycopeptide mixtures require sophisticated analysis pipelines for structural determination. Diverse software aiding the process have appeared, but their relative performance remains untested. Conducted through HUPO Human Proteome Project – Glycoproteomics Initiative, this community study, comprising both developers and users of...
Abstract A novel software, Pinnacle was used to reassess the reproducibility of a 2‐step lectin‐based O ‐glycopeptide enrichment method. publicly available dataset consisting 12 data files representing 3 technical replicates enriched glycopeptides from human serum investigated. Previously, an attempt for assessment made utilizing MS/MS scan (MS2)‐based However, stochastic nature precursor ion selection strongly biased this approach leading underestimated rate reproducibility. To bypass...