PXD015083 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD015083
- Label: PRIDE project
- Name: Assessing protein sequence database suitability using de novo sequencing