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PXD005931-1

PXD005931 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLarge scale intact glycopeptide identification by Mascot database search
DescriptionWe present the adaptability of Mascot search engine for automated identification of intact glycopeptide mass spectra. The steps involved in adopting Mascot for intact glycopeptide analysis include: i) assigning unique one letter codes for monosaccharides, ii) linearizing glycan sequences and iii) preparing custom glycoprotein databases. Stepped normalized collision energy (NCE) for HCD mostly provided both the peptide and glycan information in a single MS2 spectrum. Using standard glycoproteins, we showed that Mascot can be adopted for automated annotation of both N- and O-linked glycopeptides. In a large scale validation study, a total of 257 glycoproteins containing 970 unique glycosylation sites and 3447 non-redundant N-linked glycopeptide variants were identified in serum samples. This represent a single tool that collectively allows the i) elucidation of N- and O-linked glycopeptide spectra, ii) matching glycopeptides to known protein sequences, and iii) high-throughput, batch wise analysis of large scale glycoproteomics data sets.
HostingRepositoryPRIDE
AnnounceDate2018-02-08
AnnouncementXMLSubmission_2018-02-08_02:12:06.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRavi Chand Bollineni
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; complex glycosylation; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-02-16 01:23:39ID requested
12018-02-08 02:12:07announced
Publication List
Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B, Large-scale intact glycopeptide identification by Mascot database search. Sci Rep, 8(1):2117(2018) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: Glycoproteomics, higher-energy collisional induced dissociation (HCD), Mascot, prostate cancer, serum
Contact List
Bernd Thiede
contact affiliationUniversity of Oslo, Department of Biosciences
contact emailbernd.thiede@ibv.uio.no
lab head
Ravi Chand Bollineni
contact affiliationUniversity of Oslo
contact emailr.c.bollineni@ibv.uio.no
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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