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PXD013888 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleFast and accurate bacterial species identification in biological samples using LC-MS/MS mass spectrometry and machine learning (DIA dataset)
DescriptionWe 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.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterArnaud 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;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion ETD
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-05-16 16:04:21ID requested
12019-10-09 13:37:21announced
Publication List
no publication
Keyword List
submitter keyword: Bacterial identification, Urine, LC-MSMS, DIA, Machine Learning
Contact List
Arnaud Droit
contact affiliationCHU de Quebec Universite Laval
contact emailarnaud.droit@crchuq.ulaval.ca
lab head
Arnaud Droit
contact affiliationCHU de Quebec Universite Laval
contact emailarnaud.droit@crchuq.ulaval.ca
dataset submitter
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