PXD005931-1

PXD005931 is an original dataset announced via ProteomeXchange.

Title	Large scale intact glycopeptide identification by Mascot database search
Description	We 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.
HostingRepository	PRIDE
AnnounceDate	2018-02-08
AnnouncementXML	Submission_2018-02-08_02:12:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ravi Chand Bollineni
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; complex glycosylation; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-16 01:23:39	ID requested
⏵ 1	2018-02-08 02:12:07	announced
2	2024-10-22 04:36:22	announced	2024-10-22: Updated project metadata.

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]

curator keyword: Technical

submitter keyword: Glycoproteomics, higher-energy collisional induced dissociation (HCD), Mascot, prostate cancer, serum

Bernd Thiede
contact affiliation	University of Oslo, Department of Biosciences
contact email	bernd.thiede@ibv.uio.no
lab head
Ravi Chand Bollineni
contact affiliation	University of Oslo
contact email	r.c.bollineni@ibv.uio.no
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/02/PXD005931

PRIDE project URI

• PRIDE
  1. PXD005931
     1. Label: PRIDE project
     2. Name: Large scale intact glycopeptide identification by Mascot database search