PXD013888-1
PXD013888 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Fast and accurate bacterial species identification in biological samples using LC-MS/MS mass spectrometry and machine learning (DIA dataset) |
| Description | We have developed a new strategy for identifying bacterial species in biological samples using specific LC-MS/MS peptidic signatures. In the first training step, deep proteome coverage of bacteria of interest is obtained in Data Independent Acquisition (DIA) mode, followed by the use of machine learning to define the peptides the most susceptible to distinguish each bacterial species from the others. Then, in the second step, this peptidic signature is monitored in biological samples using targeted proteomics. This method, which allows the bacterial identification from clinical specimens in less than 4h, has been applied to 15 species representing 84% of all Urinary Tract Infections (UTI). This dataset contains all the DIA files that has been used by the machine learnings algorithms to define a peptidic signture for UTI. |
| HostingRepository | MassIVE |
| AnnounceDate | 2019-10-09 |
| AnnouncementXML | Submission_2019-10-09_13:37:20.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Arnaud Droit |
| SpeciesList | scientific name: Citrobacter freundii; NCBI TaxID: 546; scientific name: Enterobacter cloacae; NCBI TaxID: 550; scientific name: Escherichia coli K-12; NCBI TaxID: 83333; scientific name: Enterobacter aerogenes KCTC 2190; NCBI TaxID: 1028307; scientific name: Klebsiella oxytoca; NCBI TaxID: 571; scientific name: Klebsiella pneumoniae subsp. pneumoniae MGH 78578; NCBI TaxID: 272620; scientific name: Pseudomonas aeruginosa PAO1; NCBI TaxID: 208964; scientific name: Proteus mirabilis; NCBI TaxID: 584; scientific name: Enterococcus faecalis V583; NCBI TaxID: 226185; scientific name: Staphylococcus aureus subsp. aureus NCTC 8325; NCBI TaxID: 93061; scientific name: Staphylococcus epidermidis ATCC 12228; NCBI TaxID: 176280; scientific name: Staphylococcus haemolyticus JCSC1435; NCBI TaxID: 279808; scientific name: Streptococcus mitis; NCBI TaxID: 28037; scientific name: Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305; NCBI TaxID: 342451; scientific name: Streptococcus agalactiae 2603V/R; NCBI TaxID: 208435; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Orbitrap Fusion ETD |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2019-05-16 16:04:21 | ID requested | |
| ⏵ 1 | 2019-10-09 13:37:21 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Bacterial identification, Urine, LC-MSMS, DIA, Machine Learning |
Contact List
| Arnaud Droit | |
|---|---|
| contact affiliation | CHU de Quebec Universite Laval |
| contact email | arnaud.droit@crchuq.ulaval.ca |
| lab head | |
| Arnaud Droit | |
| contact affiliation | CHU de Quebec Universite Laval |
| contact email | arnaud.droit@crchuq.ulaval.ca |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/MSV000083793/ |
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