SugarQb (www.imba.oeaw.ac.at/sugarqb) is a freely available collection of computational tools for the automated identification of intact glycopeptides from high-resolution HCD MS/MS datasets in the Proteome Discoverer environment. We report the migration of SugarQb to the latest and free version of Proteome Discoverer 2.1, and apply it to the analysis of PNGase F-resistant N-glycopeptides from mouse embryonic stem cells. The analysis of intact glycopeptides highlights unexpected technical limitations to PNGase F-dependent glycoproteomic workflows at the proteome level, and warrants a critical reinterpretation of seminal datasets in the context of N-glycosylation-site prediction.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055662 | PMC |
| http://dx.doi.org/10.1002/pmic.201700436 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Bottom-Up Proteomics Workflow for Studying Multi-organism Systems.
Methods Mol Biol
December 2024
Department of Chemistry, North Carolina State University, Raleigh, NC, USA.
In recent years, discovery proteomics has emerged as a pivotal tool in biological research, especially when studying the intricate relationships among multiple organisms. To delve deeper into these interactions, we pioneered a bottom-up proteomics workflow. Using nanoLC-MS/MS and a label-free quantification method, this work specifically examines the differential protein expression in fleas (Ctenocephalides felis felis) that have been experimentally infected with Bartonella henselae, the causative agent of cat scratch disease (CSD).
View Article and Find Full Text PDFOmics analysis reveals galectin-3 to be a potential key regulator of allergic inflammation in hereditary angioedema.
J Allergy Clin Immunol Glob
February 2025
Department of Medicine, Division of Allergy, Immunology & Rheumatology, Jacobs School of Medicine and Biomedical Sciences, Clinical Translational Research Center, University at Buffalo, Buffalo, NY.
Background: Hereditary angioedema (HAE) is a rare inherited disorder that predisposes an individual to develop vasogenic edema. Bradykinin release, which increases vascular permeability, results in angioedema. C1 esterase inhibitor (C1-INH) is a major regulator of critical enzymes involved in bradykinin generation and mutations in genes that encode the C1 inhibitor of complement factor 1, which prevent its synthesis (type I HAE), form a dysfunctional protein (type II HAE), or have normal functioning C1-INH (type III HAE, aka HAE-III).
View Article and Find Full Text PDFUltradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.
Proc Natl Acad Sci U S A
November 2024
Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007.
As a unique type of glycosylation, O-linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation) on Ser/Thr residues of proteins was discovered 40 y ago. O-GlcNAcylation is catalyzed by two enzymes: O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), which add and remove O-GlcNAc, respectively. O-GlcNAcylation is an essential glycosylation that regulates the functions of many proteins in virtually all cellular processes.
View Article and Find Full Text PDFSerum proteomics for the identification of biomarkers to flag predilection of COVID19 patients to various organ morbidities.
Clin Proteomics
November 2024
Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
Background: COVID19 is a pandemic that has affected millions around the world since March 2020. While many patients recovered completely with mild illness, many patients succumbed to various organ morbidities. This heterogeneity in the clinical presentation of COVID19 infection has posed a challenge to clinicians around the world.
View Article and Find Full Text PDFThe leucine-rich repeat receptor kinase QSK1 regulates PRR-RBOHD complexes targeted by the bacterial effector HopF2Pto.
Plant Cell
October 2024
Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa 230-0045, Japan.
Article Synopsis
- Plants use pattern recognition receptors (PRRs) like EFR and FLS2 to detect bacterial pathogens and activate their immune response via RBOHD.
- QSK1, identified as a protein associated with the PRR-RBOHD complex, acts as a negative regulator by downregulating EFR and FLS2, leading to suppressed immunity.
- The bacterial effector HopF2Pto manipulates QSK1 to inhibit immune responses, demonstrating the sophisticated interplay between plant defense mechanisms and pathogen strategies.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!