PXD015083

PXD015083 is an original dataset announced via ProteomeXchange.

Title	Assessing protein sequence database suitability using de novo sequencing
Description	The analysis of samples from unsequenced and/or understudied species as well as samples where the proteome is derived from multiple organisms poses two key questions. The first is whether the proteomic data obtained from an unusual sample type even contains peptide tandem mass spectra. The second question is whether an appropriate protein sequence database is available for proteomic searches. We describe the use of automated de novo sequencing for evaluating both the quality of a collection of tandem mass spectra and the suitability of a given protein sequence database for searching that data. Applications of this method include the proteome analysis of closely related species, metaproteomics, and proteomics of extant organisms.
HostingRepository	PRIDE
AnnounceDate	2020-02-13
AnnouncementXML	Submission_2020-09-28_00:24:33.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD015083
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Richard Johnson
SpeciesList	scientific name: Ursus deningeri; NCBI TaxID: 518691; scientific name: marine metagenome; NCBI TaxID: 408172; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Hydrolagus colliei; NCBI TaxID: 7873; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Diaphorina citri (Asian citrus psyllid); NCBI TaxID: 121845; scientific name: glacier metagenome; NCBI TaxID: 1651087; scientific name: Leucoraja erinacea; NCBI TaxID: 7782;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-20 01:50:21	ID requested
1	2020-02-12 03:48:43	announced
2	2020-02-13 00:44:11	announced	2020-02-13: Updated project metadata.
⏵ 3	2020-09-28 00:24:34	announced	2020-02-13: Updated project metadata. 2020-09-28: Updated publication reference for PubMed record(s): 31732549.

Johnson RS, Searle BC, Nunn BL, Gilmore JM, Phillips M, Amemiya CT, Heck M, MacCoss MJ, Sequencing. Mol Cell Proteomics, 19(1):198-208(2020) [pubmed]

curator keyword: Technical

submitter keyword: proteomics, metaproteomics, fasta

Michael J. MacCoss
contact affiliation	Department of Genome Sciences, University of Washington, Seattle, WA, United States
contact email	maccoss@uw.edu
lab head
Richard Johnson
contact affiliation	University of Washington
contact email	rj8@uw.edu
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/2019/11/PXD015083

PRIDE project URI

• PRIDE
  1. PXD015083
     1. Label: PRIDE project
     2. Name: Assessing protein sequence database suitability using de novo sequencing