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PXD015083

PXD015083 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAssessing protein sequence database suitability using de novo sequencing
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2020-02-13
AnnouncementXMLSubmission_2020-09-28_00:24:33.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD015083
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterRichard 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;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion; Q Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-08-20 01:50:21ID requested
12020-02-12 03:48:43announced
22020-02-13 00:44:11announced2020-02-13: Updated project metadata.
32020-09-28 00:24:34announced2020-02-13: Updated project metadata.
2020-09-28: Updated publication reference for PubMed record(s): 31732549.
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: proteomics, metaproteomics, fasta
Contact List
Michael J. MacCoss
contact affiliationDepartment of Genome Sciences, University of Washington, Seattle, WA, United States
contact emailmaccoss@uw.edu
lab head
Richard Johnson
contact affiliationUniversity of Washington
contact emailrj8@uw.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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