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PXD010000

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2018-06-13
  • AnnouncementXML: Submission_2018-06-13_03:00:16.xml
  • DigitalObjectIdentifier: http://dx.doi.org/10.6019/PXD010000
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Supported dataset by repository
  • PrimarySubmitter: Matthew Monroe
  • Title: DeNovo Peptide Identification Deep Learning Training Set
  • Description: A benchmark set of bottom-up proteomics data for training deep learning networks. It has data from 51 organisms and includes nearly 1 million peptides.
  • SpeciesList: scientific name: Cellvibrio gilvus (strain ATCC 13127 / NRRL B-14078); NCBI TaxID: 593907; scientific name: Shewanella oneidensis (strain MR-1); NCBI TaxID: 211586; scientific name: Francisella tularensis subsp. novicida (strain U112); NCBI TaxID: 401614; scientific name: Cyanobacterium stanieri; NCBI TaxID: 102235; scientific name: Prevotella ruminicola (strain ATCC 19189 / JCM 8958 / 23); NCBI TaxID: 264731; scientific name: Faecalibacterium prausnitzii SL3/3; NCBI TaxID: 657322; scientific name: Campylobacter jejuni; NCBI TaxID: 197; scientific name: Pseudomonas putida (strain KT2440); NCBI TaxID: 160488; scientific name: Cellulophaga baltica 18; NCBI TaxID: 1348584; scientific name: Bacillus subtilis (strain 168); NCBI TaxID: 224308; scientific name: Legionella pneumophila; NCBI TaxID: 446; scientific name: Streptomyces sp.; NCBI TaxID: 1931; scientific name: Dorea formicigenerans; NCBI TaxID: 39486; scientific name: Cupriavidus necator (strain ATCC 43291 / DSM 13513 / N-1) (Ralstonia eutropha); NCBI TaxID: 1042878; scientific name: Sulfobacillus thermosulfidooxidans; NCBI TaxID: 28034; scientific name: Alcaligenes faecalis; NCBI TaxID: 511; scientific name: Bacillus subtilis subsp. subtilis str. NCIB 3610; NCBI TaxID: 535026; scientific name: Methylomicrobium alcaliphilum (strain DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z); NCBI TaxID: 1091494; scientific name: Paracoccus denitrificans; NCBI TaxID: 266; scientific name: Rhodococcus sp. (strain RHA1); NCBI TaxID: 101510; scientific name: Mycobacterium smegmatis; NCBI TaxID: 1772; scientific name: Paenibacillus polymyxa ATCC 842; NCBI TaxID: 1036171; scientific name: Acidiphilium cryptum (strain JF-5); NCBI TaxID: 349163; NCBI TaxID: 1666912; scientific name: Bacillus cereus (strain ATCC 14579 / DSM 31); NCBI TaxID: 226900; scientific name: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482); NCBI TaxID: 226186; scientific name: Lactobacillus casei subsp. casei ATCC 393; NCBI TaxID: 219334; NCBI TaxID: 1486246; scientific name: Streptomyces griseorubens; NCBI TaxID: 66897; NCBI TaxID: 1798193; scientific name: Micrococcus luteus (Micrococcus lysodeikticus); NCBI TaxID: 1270; scientific name: Stigmatella aurantiaca (strain DW4/3-1); NCBI TaxID: 378806; scientific name: Anaerococcus hydrogenalis DSM 7454; NCBI TaxID: 561177; scientific name: Citrobacter freundii; NCBI TaxID: 546; scientific name: Myxococcus xanthus DZ2; NCBI TaxID: 1198133; scientific name: Rhodopseudomonas palustris; NCBI TaxID: 1076; scientific name: Chryseobacterium indologenes; NCBI TaxID: 253; scientific name: Bacteroides fragilis (strain 638R); NCBI TaxID: 862962; scientific name: Bifidobacterium bifidum DSM 20456 = JCM 1255; NCBI TaxID: 500634; scientific name: Coprococcus comes ATCC 27758; NCBI TaxID: 470146; scientific name: Listeria monocytogenes serotype 1/2a (strain 10403S); NCBI TaxID: 393133; scientific name: Ruminococcus gnavus ATCC 29149; NCBI TaxID: 411470; scientific name: Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12); NCBI TaxID: 391904; scientific name: Streptococcus agalactiae; NCBI TaxID: 1311; scientific name: Fibrobacter succinogenes (strain ATCC 19169 / S85); NCBI TaxID: 59374; scientific name: Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2); NCBI TaxID: 1140; scientific name: Clostridium ljungdahlii (strain ATCC 55383 / DSM 13528 / PETC); NCBI TaxID: 748727; scientific name: Delftia acidovorans (strain DSM 14801 / SPH-1); NCBI TaxID: 398578; scientific name: Rhizobium radiobacter (Agrobacterium tumefaciens) (Agrobacterium radiobacter); NCBI TaxID: 358; scientific name: Algoriphagus marincola HL-49; NCBI TaxID: 1305737;
  • ModificationList: Oxidation
  • Instrument: Q Exactive

Dataset History

VersionDatetimeStatusChangeLog Entry
02018-06-01 02:05:00ID requested
12018-06-13 03:00:16announced

Publication List

  1. Dataset with its publication pending

Keyword List

  1. submitter keyword: machine learning, deep learning, bacterial diversity

Contact List

    Samuel Payne
    • contact affiliation: Pacific Northwest National Laboratory
    • contact email: samuel.payne@pnnl.gov
    • lab head:
    Matthew Monroe
    • contact affiliation: Pacific Northwest National Laboratory
    • contact email: matthew.monroe@pnnl.gov
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
Repository Record List
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