PXD039320

PXD039320 is an original dataset announced via ProteomeXchange.

Title	Shotgun Proteomics Analysis, Functional Networks and Peptide Biomarkers for Biogenic Amine-producing Bacteria
Description	Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds, such as histamine, cadaverine, tyramine and putrescine, after foods spoil due to microorganisms. In the present work, we applied a shotgun proteomics approach to quickly and easily characterize 15 different foodborne strains of biogenic amine-producing bacteria. A total of 10673 peptide spectrum matches (PSMs) belonging to 4081 nonredundant peptides and corresponding to 1811 annotated proteins were identified. With the results, relevant functional pathways were determined and the strains were differentiated into different Euclidean hierarchical clusters. Moreover, a predicted protein‒protein interaction network of biogenic amine foodborne strains was created. The whole confidence network contains 260 nodes and 1973 interactions. Most of the identified proteins were related to pathways and networks of energy, putrescine metabolism and host‒virus interaction. In addition, a total of 556 nonredundant peptides were identified as virulence factors, and most of these peptides corresponded to functions such as toxins, antimicrobial compound production, antimicrobial resistance, additional resistances and tolerances, host colonization and immune evasion, ABC transporters, phage proteins, and alternative virulence factors and proteins involved in horizontal transfer. Potential species-specific peptide biomarkers were screened. Thus, 77 species-specific peptide biomarkers belonging to 64 different proteins were proposed to identify 10 species (Enterobacter aerogenes, Enterobacter cloacae, Hafnia alvei, Klebsiella oxytoca, Morganella morganii, Proteus mirabilis, Proteus penneri, Proteus vulgaris, Raoutella planticola, Stenotrophomonas maltophilia). All of these results constitute the first major dataset of peptides and proteins of seafood biogenic amine-producing strains. This repository may be useful for further studies, for the development of new therapeutic treatments for food intoxication and for tracking microbial sources in foodstuffs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:56:33.122.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD039320
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Mónica Carrera
SpeciesList	scientific name: Proteus vulgaris; NCBI TaxID: 585; scientific name: Morganella morganii (Proteus morganii); NCBI TaxID: 582; scientific name: Raoultella planticola; NCBI TaxID: 575; scientific name: Enterobacter cloacae EcWSU1; NCBI TaxID: 1045856; scientific name: Proteus mirabilis; NCBI TaxID: 584; scientific name: Stenotrophomonas maltophilia; NCBI TaxID: 40324; scientific name: Enterobacter sp. T3; NCBI TaxID: 640459; scientific name: Klebsiella oxytoca; NCBI TaxID: 571; scientific name: Proteus penneri; NCBI TaxID: 102862; scientific name: Hafnia alvei; NCBI TaxID: 569;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-09 02:09:08	ID requested
1	2023-07-20 11:39:00	announced
2	2023-11-14 09:03:39	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:56:34	announced	2024-10-22: Updated project metadata.

10.6019/PXD039320;

10.3390/ijms24097704;

Abril AG, Calo-Mata P, B, ö, hme K, Villa TG, Barros-Vel, á, zquez J, Pazos M, Carrera M, Shotgun Proteomics Analysis, Functional Networks, and Peptide Biomarkers for Seafood-Originating Biogenic-Amine-Producing Bacteria. Int J Mol Sci, 24(9):(2023) [pubmed]

submitter keyword: LC‒ESI‒MS/MS, shotgun proteomics, mass spectrometry,Biogenic amine-producing bacteria, food, bacterial detection and identification, seafood

Mónica Carrera
contact affiliation	Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
contact email	mcarrera@iim.csic.es
lab head
Mónica Carrera
contact affiliation	CSIC
contact email	mcarrera@iim.csic.es
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/2023/07/PXD039320

PRIDE project URI

• PRIDE
  1. PXD039320
     1. Label: PRIDE project
     2. Name: Shotgun Proteomics Analysis, Functional Networks and Peptide Biomarkers for Biogenic Amine-producing Bacteria