ArticleNature methods2021
Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.
Erratum issuedAbstract readEvaluation Study
In one paragraph
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 88 papers.
0numbers the graph read from it
0cells of the map it votes in
88citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
88 citing papers in PubMed.
- Article
- Article
- Large glycomics datasets as a tool to understand the function of glycans.Nature chemical biology · 2026Review
- GlycoDiveR: A Modular R Framework to Analyze and Visualize Highly Dimensional Glycoproteomics Data.ACS measurement science au · 2026Article
- UnderstandingJournal of the American Society for Mass Spectrometry · 2026Article
- GlycoDiveR: a modular R framework to analyze and visualize highly dimensional glycoproteomics data.bioRxiv : the preprint server for biology · 2026Article
- Profiling Glycoproteins Enriched by Multinanoparticle Protein Corona.Analytical chemistry · 2026Article
- PredictiveACS omega · 2026Article
- Mass Spectrometry Analysis of Biotherapeutic Monoclonal Antibody Glycosylation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integrative Analysis of Fucosylated Tetra Glycoforms in Hepatocellular Carcinoma: A NanoLC-PRM-MS/MS and Machine Learning Approach.Journal of proteome research · 2025Article
- Epigenetic regulatory mechanisms of autoimmune skin diseases: novel biomarkers and therapeutic prospects.Clinical epigenetics · 2025Review
- Extracting informative glycan-specific ions from glycopeptide MS/MS spectra with GlyCounter.bioRxiv : the preprint server for biology · 2025Article
- Analytical dissection of minor glycoforms and glycoprotein associations in rAAV preparations by multimodal glycoproteomics.Analytical and bioanalytical chemistry · 2025Article
- Absolute Quantitation of Phosphopeptides and Glycopeptides Using Coulometric Mass Spectrometry.ACS measurement science au · 2025Article
- Article
- Engineering glycosyltransferases into glycan binding proteins using a mammalian surface display platform.Nature communications · 2025Article
- Ultradeep N-glycoproteome atlas of mouse reveals spatiotemporal signatures of brain aging and neurodegenerative diseases.Nature communications · 2025Article
- Accelerating the stride toward functional glycoproteomics.Trends in biochemical sciences · 2025Article
- Poly-sialylated glycan of cervicovaginal fluid can be a potential marker of preterm birth.Scientific reports · 2025Article
- Comparative analysis of glycoproteomic software using a tailored glycan database.Analytical and bioanalytical chemistry · 2025Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
54 authors.
Rebeca KawaharaDepartment of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0002-0292-2637
Anastasia ChernykhDepartment of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0002-1493-6964
Kathirvel AlagesanInstitute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia.
Marshall BernProtein Metrics Inc., Cupertino, CA, USA.ORCID http://orcid.org/0000-0003-0342-9390
Weiqian CaoInstitutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-1007-4607
Robert J ChalkleyUCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-9757-7302
Kai ChengState University of New York, Buffalo, NY, USA.
Matthew S ChooAnalytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.ORCID http://orcid.org/0000-0002-1376-3352
Nathan EdwardsClinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA.
Radoslav GoldmanClinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA.
Marcus HoffmannMax Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
Yingwei HuDepartment of Pathology, The Johns Hopkins University, Baltimore, MD, USA.
Yifan HuangDepartment of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
Jin Young KimResearch Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea.ORCID http://orcid.org/0000-0002-0656-1269
Doron KletterProtein Metrics Inc., Cupertino, CA, USA.
Benoit LiquetDepartment of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia.
Mingqi LiuInstitutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.
Yehia MechrefDepartment of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
Bo MengState Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China.
Sriram NeelameghamState University of New York, Buffalo, NY, USA.ORCID http://orcid.org/0000-0002-1371-8500
Terry Nguyen-KhuongAnalytics Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore.ORCID http://orcid.org/0000-0002-5852-542X
Jonas NilssonProteomics Core Facility, Sahlgrenska academy, University of Gothenburg, Gothenburg, Sweden.ORCID http://orcid.org/0000-0001-5263-2454
Adam PapBRC, Laboratory of Proteomics Research, Szeged, Hungary.
Gun Wook ParkResearch Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea.
Benjamin L ParkerDepartment of Anatomy and Physiology, University of Melbourne, Melbourne, VIC, Australia.
Cassandra L PeggSchool of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia.
Josef M PenningerIMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria.ORCID http://orcid.org/0000-0002-8194-3777
Toan K PhungSchool of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia.ORCID http://orcid.org/0000-0002-2964-6070
Markus PiochMax Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
Erdmann RappMax Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.ORCID http://orcid.org/0000-0001-6618-2626
Enes SakalliIMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria.
Miloslav SandaClinical and Translational Glycoscience Research Center (CTGRC), Georgetown University, Washington, DC, USA.ORCID http://orcid.org/0000-0002-7735-3635
Benjamin L SchulzSchool of Chemistry and Molecular Biosciences, University of Queensland, Queensland, QLD, Australia.ORCID http://orcid.org/0000-0002-4823-7758
Nichollas E ScottDeparment of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia.ORCID http://orcid.org/0000-0003-2556-8316
Georgy SofronovDepartment of Mathematics and Statistics, Macquarie University, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0001-5342-7559
Johannes StadlmannIMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria.
Sergey Y VakhrushevCopenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-0418-5765
Christina M WooDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8687-9105
Hung-Yi WuDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Pengyuan YangInstitutes of Biomedical Sciences, and the NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0001-5779-1008
Wantao YingState Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China.
Hui ZhangDepartment of Pathology, The Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-8726-7098
Yong ZhangState Key Laboratory of Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, China.ORCID http://orcid.org/0000-0003-0513-8941
Jingfu ZhaoDepartment of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
Joseph ZaiaDepartment of Biochemistry, Boston University Medical Campus, Boston, MA, USA.ORCID http://orcid.org/0000-0001-9497-8701
Stuart M HaslamDepartment of Life Sciences, Imperial College London, London, UK.ORCID http://orcid.org/0000-0002-5563-679X
Giuseppe PalmisanoInstituto de Ciências Biomédicas, Departamento de Parasitologia, Universidade de São Paulo, São Paulo, SP, Brazil.
Jong Shin YooResearch Center of Bioconvergence Analysis, Korea Basic Science Institute, Daejeon, Republic of Korea.
Göran LarsonDepartment of Laboratory Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.ORCID http://orcid.org/0000-0002-2616-0366
Kai-Hooi KhooInstitute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.ORCID http://orcid.org/0000-0003-2906-406X
Katalin F MedzihradszkyUCSF, School of Pharmacy, Department of Pharmaceutical Chemistry, San Francisco, CA, USA.
Daniel KolarichInstitute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, Australia.ORCID http://orcid.org/0000-0002-8452-1350
Nicolle H PackerDepartment of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.ORCID http://orcid.org/0000-0002-7532-4021
Morten Thaysen-AndersenDepartment of Molecular Sciences, Macquarie University, Sydney, NSW, Australia. morten.andersen@mq.edu.au.ORCID http://orcid.org/0000-0001-8327-6843
Funding
Systems Biology of GlycosylationR01HL103411 · NHLBI · STATE UNIVERSITY OF NEW YORK AT BUFFALO · PI NEELAMEGHAM, SRIRAM · 2011 to 2025
$7.1MGlycoprotein biomarkers for the early detection of aggressive prostate cancerU01CA152813 · NCI · JOHNS HOPKINS UNIVERSITY · PI ZHANG, HUI · 2010 to 2021
$6.2MThe Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic TargetsU24CA210985 · NCI · JOHNS HOPKINS UNIVERSITY · PI CHAN, DANIEL WANYUI, ZHANG, HUI · 2016 to 2020
$5.3MO-glycoproteins in the progression of liver diseaseR01CA238455 · NCI · GEORGETOWN UNIVERSITY · PI GOLDMAN, RADOSLAV · 2019 to 2023
$2.6MLC-MS Analysis of Site Specific Protein GlycoformsU01CA230692 · NCI · GEORGETOWN UNIVERSITY · PI EDWARDS, NATHAN J, GOLDMAN, RADOSLAV · 2018 to 2020
$1.3MOrbitrap Fusion Lumos ETDS10OD023557 · OD · GEORGETOWN UNIVERSITY · PI GOLDMAN, RADOSLAV · 2017 to 2017
$1.1MNCI NIH HHS R01 CA238455NCI NIH HHS U01 CA152813NCI NIH HHS U01 CA230692NCI NIH HHS U24 CA210985NHLBI NIH HHS R01 HL103411NIH HHS S10 OD023557
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 the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.
Indexed as
SoftwareGlycopeptidesGlycoproteinsGlycosylationHumansInformaticsProteomeProteomicsResearch PersonnelTandem Mass SpectrometryGlycopeptidesGlycoproteinsProteome
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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 Socratic graph.