PXD010000-2

PXD010000 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:45:45.751.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD010000
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew Monroe
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: bacteria; NCBI TaxID: 1666912; scientific name: Campylobacter jejuni; NCBI TaxID: 197; scientific name: Cellulophaga baltica 18; NCBI TaxID: 1348584; 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: Bacillus subtilis subsp. subtilis str. NCIB 3610; NCBI TaxID: 535026; scientific name: Alcaligenes faecalis; NCBI TaxID: 511; 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: Pseudomonas putida KT2440; NCBI TaxID: 160488; scientific name: Paenibacillus polymyxa ATCC 842; NCBI TaxID: 1036171; scientific name: Acidiphilium cryptum (strain JF-5); NCBI TaxID: 349163; 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; scientific name: Streptomyces griseorubens; NCBI TaxID: 66897; scientific name: Fibrobacter succinogenes subsp. succinogenes S85; NCBI TaxID: 59374; scientific name: Micrococcus luteus (Micrococcus lysodeikticus); NCBI TaxID: 1270; scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308; scientific name: Stigmatella aurantiaca (strain DW4/3-1); NCBI TaxID: 378806; scientific name: bacteria; NCBI TaxID: 1486246; 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: Ruminococcus gnavus ATCC 29149; NCBI TaxID: 411470; scientific name: Coprococcus comes ATCC 27758; NCBI TaxID: 470146; scientific name: Listeria monocytogenes serotype 1/2a (strain 10403S); NCBI TaxID: 393133; 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: 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: bacteria; NCBI TaxID: 1798193; 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

Revision	Datetime	Status	ChangeLog Entry
0	2018-06-01 02:05:00	ID requested
1	2018-06-13 03:00:16	announced
⏵ 2	2024-10-22 04:45:46	announced	2024-10-22: Updated project metadata.

10.6019/PXD010000;

ProteomeXchange project tag: benchmarking, machine learning

submitter keyword: bacterial diversity,machine learning, deep learning

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

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/2018/06/PXD010000

PRIDE project URI

• PRIDE
  1. PXD010000
     1. Label: PRIDE project
     2. Name: DeNovo Peptide Identification Deep Learning Training Set