PXD014522

PXD014522 is an original dataset announced via ProteomeXchange.

Title	Discovery of species-unique peptide biomarkers of bacterial pathogens by tandem mass spectrometry-based proteotyping
Description	Respiratory-tract infections are a predominant cause for clinical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for bacterial pathogens commonly found in respiratory tract infections: Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure-culture bacterial reference strains, reflecting the genomic variation in the four species and, furthermore in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. Peptide biomarker candidates for each species is presented. As a proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, demonstrating their potential as effective peptide biomarker candidates for diagnostics of infectious diseases.
HostingRepository	PRIDE
AnnounceDate	2020-01-17
AnnouncementXML	Submission_2020-01-17_06:55:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sahlgrenska Academy Proteomics Core
SpeciesList	scientific name: Streptococcus pneumoniae R6; NCBI TaxID: 171101; scientific name: Moraxella catarrhalis; NCBI TaxID: 480; scientific name: Haemophilus influenzae; NCBI TaxID: 727; scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-08 08:19:42	ID requested
⏵ 1	2020-01-17 06:55:15	announced

Karlsson R, Thorsell A, Gomila M, Salv, à, -Serra F, Jakobsson HE, Gonzales-Siles L, Ja, é, n-Luchoro D, Skovbjerg S, Fuchs J, Karlsson A, Boulund F, Johnning A, Kristiansson E, Moore ERB, Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping. Mol Cell Proteomics, 19(3):518-528(2020) [pubmed]

submitter keyword: Bacteria, Staphylococcus aureus, Moraxella catarrhalis, Haemophilus influenzae, Streptococcus pneumoniae, proteotyping,

Roger Karlsson
contact affiliation	PhD, Consultant at Nanoxis Consulting AB, Gothenburg, Sweden
contact email	roger.karlsson@nanoxisconsulting.com
lab head
Sahlgrenska Academy Proteomics Core
contact affiliation	University of Gothenburg
contact email	egor.vorontsov@gu.se
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/2020/01/PXD014522

PRIDE project URI

• PRIDE
  1. PXD014522
     1. Label: PRIDE project
     2. Name: Discovery of species-unique peptide biomarkers of bacterial pathogens by tandem mass spectrometry-based proteotyping