PXD011723 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | MS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments |
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_02:16:14.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD011723 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Nicola Ternette |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | DTT_C; Hex; Methylphosphonate; Delta:H(4)C(2)O(-1)S(1); DFDNB; Propionamide; GlycerylPE; LeuArgGlyGly; Deamidated; sulfo+amino; Methylpyrroline; Trp->Oxolactone; Methylamine; Myristoyl; Cation:K; Gln->pyro-Glu; Met->Hsl; Guanidinyl; Menadione-HQ; DAET; Dehydro; Trimethyl; Ammonia-loss; Oxidation; Diphthamide; AEC-MAEC; Carboxy; O-pinacolylmethylphosphonate; Ethanolamine; Cation:Na; Trp->Hydroxykynurenin; Sulfo; GlyGly; Deoxy; Methyl+Deamidated; Glutathione; Formyl; Carbamyl; Cation:Mg[II]; Sulfide; NDA; Amino; Ammonium; Dimethyl; Delta:H(5)C(2); Lipoyl; Hypusine; Crotonaldehyde; Met->Hse; Dethiomethyl; Cytopiloyne; Amidated; Thioacyl; Diethyl; Lys->AminoadipicAcid; Pro->pyro-Glu; Ethanolyl; Phospho; Acetyl; Palmitoyl; Cation:Ni[II]; ADP-Ribosyl; Methylthio; Carboxymethyl; HexNAc; Carbamidomethyl; Cysteinyl; Glu->pyro-Glu; CarboxymethylDTT; Carboxyethyl; Hydroxymethyl; CAF; Delta:H(2)C(2); Ethyl; Cation:Li; O-Isopropylmethylphosphonate; SulfurDioxide; Isopropylphospho; Methyl; AEBS; Dihydroxyimidazolidine; Phosphopropargyl; Ethoxyformyl; Didehydro; Trp->Kynurenin; Pro->Pyrrolidinone; Iminobiotin; SMA; Arg2PG; Lys->Allysine; Farnesyl; Amidine; ethylamino; maleimide; O-Methylphosphate; Dehydrated; Biotin; Dioxidation; Ethyl+Deamidated; Carbofuran; glycidamide |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-11-19 07:51:20 | ID requested | |
⏵ 1 | 2019-01-02 02:16:16 | 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] |
Keyword List
ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project |
curator keyword: Technical, Biomedical |
submitter keyword: Immunopeptidome |
HLA |
LC-MS/MS |
NetMHCpan |
Binding Prediction |
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/PXD011723 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD011723
- Label: PRIDE project
- Name: MS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments