ArticleAnalytical chemistry2014
New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets.
Article in Analytical chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Recent Advances in Software Tools for More Generic and Precise Intact Glycopeptide Analysis.Molecular & cellular proteomics : MCP · 2021Pooled it
- GPBD: high-confidence N-glycopeptide identification via glycopeptide boundary discriminator.Analytical and bioanalytical chemistry · 2025Article
- GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching.Journal of proteome research · 2023Article
- Site-Specific Intact N-Linked Glycopeptide Characterization of Prostate-Specific Membrane Antigen from Metastatic Prostate Cancer Cells.ACS omega · 2022Article
- The Need for Community Standards to Enable Accurate Comparison of Glycoproteomics Algorithm Performance.Molecules (Basel, Switzerland) · 2021Article
- GlycoHybridSeq: Automated Identification of N-Linked Glycopeptides Using Electron Transfer/High-Energy Collision Dissociation (EThcD).Journal of proteome research · 2021Article
- Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation.Molecular & cellular proteomics : MCP · 2021Review
- Glycan Compositions with GlyConnect Compozitor to Enhance Glycopeptide Identification.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Calculating Glycoprotein Similarities From Mass Spectrometric Data.Molecular & cellular proteomics : MCP · 2021Review
- DecoyDeveloper: An On-Demand, De Novo Decoy Glycopeptide Generator.Journal of proteome research · 2019Article
- Advances in mass spectrometry-based glycoproteomics.Electrophoresis · 2018Review
- Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE.Journal of the American Society for Mass Spectrometry · 2018Article
- Large-scale intact glycopeptide identification by Mascot database search.Scientific reports · 2018Article
- The Role of Electron Transfer Dissociation in Modern Proteomics.Analytical chemistry · 2018Review
- Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides.Journal of proteome research · 2017Article
- Algorithms and design strategies towards automated glycoproteomics analysis.Mass spectrometry reviews · 2017Review
- A LC-MS All-in-One Workflow for Site-Specific Location, Identification and Quantification of N-/O- Glycosylation in Human Chorionic Gonadotropin Drug Products.The AAPS journal · 2017Article
- Glycoprotein Enrichment Analytical Techniques: Advantages and Disadvantages.Methods in enzymology · 2017Article
- Recent advances in mass spectrometric analysis of glycoproteins.Electrophoresis · 2017Review
- MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Glycoproteins are biologically significant large molecules that participate in numerous cellular activities. In order to obtain site-specific protein glycosylation information, intact glycopeptides, with the glycan attached to the peptide sequence, are characterized by tandem mass spectrometry (MS/MS) methods such as collision-induced dissociation (CID) and electron transfer dissociation (ETD). While several emerging automated tools are developed, no consensus is present in the field about the best way to determine the reliability of the tools and/or provide the false discovery rate (FDR). A common approach to calculate FDRs for glycopeptide analysis, adopted from the target-decoy strategy in proteomics, employs a decoy database that is created based on the target protein sequence database. Nonetheless, this approach is not optimal in measuring the confidence of N-linked glycopeptide matches, because the glycopeptide data set is considerably smaller compared to that of peptides, and the requirement of a consensus sequence for N-glycosylation further limits the number of possible decoy glycopeptides tested in a database search. To address the need to accurately determine FDRs for automated glycopeptide assignments, we developed GlycoPep Evaluator (GPE), a tool that helps to measure FDRs in identifying glycopeptides without using a decoy database. GPE generates decoy glycopeptides de novo for every target glycopeptide, in a 1:20 target-to-decoy ratio. The decoys, along with target glycopeptides, are scored against the ETD data, from which FDRs can be calculated accurately based on the number of decoy matches and the ratio of the number of targets to decoys, for small data sets. GPE is freely accessible for download and can work with any search engine that interprets ETD data of N-linked glycopeptides. The software is provided at https://desairegroup.ku.edu/research.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.