PXD011794

PXD011794 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	MS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments, part 2
Description	We propose a new pipeline for the refinement of spectrum-peptide assignment, designed specifically for MHC ligand identification. By modeling the peptidome as a collection of a limited number of specificities, corresponding to the MHC alleles of the cell line, our method achieves increased sequencing depth, while at the same time removing potential experimental outliers and contaminants.
HostingRepository	PRIDE
AnnounceDate	2019-01-02
AnnouncementXML	Submission_2019-01-02_02:21:02.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD011794
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Nicola Ternette
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	Fluoro; Cation:Li; Ethyl; HCysThiolactone; Amidated; Isopropylphospho; Methyl; Cys->Dha; Hex; AEBS; Oxidation; Ethanolyl; Carboxy; Pyridylethyl; Propionamide; Phospho; Cation:Na; Deamidated; Palmitoleyl; Acetyl; Sulfo; Myristoyl; Cys->Oxoalanine; Formyl; Carbamyl; Cysteinyl; Amidine; Guanidinyl; Ammonium; Dehydrated; Biotin; Dimethyl; Dioxidation; MercaptoEthanol; Carbofuran; Trimethyl
Instrument	Orbitrap Fusion Lumos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-22 01:16:44	ID requested
⏵ 1	2019-01-02 02:21:03	announced

Publication List

Andreatta M, Nicastri A, Peng X, Hancock G, Dorrell L, Ternette N, Nielsen M, MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments. Proteomics, 19(4):e1800357(2019) [pubmed]

Andreatta M, Nicastri A, Peng X, Hancock G, Dorrell L, Ternette N, Nielsen M, MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments. Proteomics, 19(4):e1800357(2019) [pubmed]

Keyword List

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project
curator keyword: Technical, Biomedical
submitter keyword: MHC, immunopeptidomics, TC-1

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

curator keyword: Technical, Biomedical

submitter keyword: MHC, immunopeptidomics, TC-1

Contact List

Nicola Ternette
contact affiliation	The Jenner Institute Nuffield Department of Medicine University of Oxford
contact email	nicola.ternette@ndm.ox.ac.uk
lab head
Nicola Ternette
contact affiliation	University of Oxford
contact email	nicola.ternette@ndm.ox.ac.uk
dataset submitter

Full Dataset Link List

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/2019/01/PXD011794
PRIDE project URI

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/2019/01/PXD011794

PRIDE project URI

Repository Record List

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