PXD004321

PXD004321 is an original dataset announced via ProteomeXchange.

Title	TCUP: Typing and characterization of bacteria using bottom-up tandem mass spectrometry proteomics
Description	Methods for rapid and reliable microbial identification are essential in modern healthcare. The ability to detect and correctly identify pathogenic species and their resistance phenotype is necessary for accurate diagnosis and efficient treatment of infectious diseases. Bottom-up tandem mass spectrometry (MS) proteomics enables rapid characterization of large parts of the expressed genes of microorganisms. The generated data is however highly fragmented, making down-stream analyses complex. Here we present TCUP, a new computational method for typing and characterizing bacteria using proteomics data from bottom-up tandem MS. TCUP compares the generated protein sequence data to reference databases and automatically finds peptides suitable for characterization of taxonomic composition and identification of expressed antimicrobial resistance genes. TCUP was evaluated using four clinically relevant bacterial species (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae), using both simulated data generated by in silico peptide digestion and experimental proteomics data generated by liquid chromatography-tandem mass spectrometry (MS/MS). The results showed that TCUP performs correct peptide classifications at rates between 90.3% and 98.5% at the species level. The method was also able to accurately estimate the relative abundances of individual species in mixed cultures. Furthermore, TCUP could identify expressed beta-lactamases in an ESBL-producing E. coli strain, even when the strain was cultivated in the absence of antibiotics on non-selective media. Finally, TCUP is computationally efficient, easy to integrate in existing bioinformatics workflows and freely available under an open source license for both Windows and Linux environments.
HostingRepository	PRIDE
AnnounceDate	2017-04-20
AnnouncementXML	Submission_2017-04-20_03:56:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fredrik Boulund
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-06-13 06:44:51	ID requested
⏵ 1	2017-04-20 03:56:09	announced

Boulund F, Karlsson R, Gonzales-Siles L, Johnning A, Karami N, Al-Bayati O, Å, hr, é, n C, Moore ERB, Kristiansson E, Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics. Mol Cell Proteomics, 16(6):1052-1063(2017) [pubmed]

curator keyword: Technical, Biological

submitter keyword: proteotyping, bottom-up, tandem mass spectrometry

Edward, R. B. Moore
contact affiliation	Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Gothenburg, Sweden
contact email	erbmoore@ccug.se
lab head
Fredrik Boulund
contact affiliation	Chalmers University of Technology
contact email	fredrik.boulund@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004321
     1. Label: PRIDE project
     2. Name: TCUP: Typing and characterization of bacteria using bottom-up tandem mass spectrometry proteomics