PXD053879

PXD053879 is an original dataset announced via ProteomeXchange.

Title	Porin expression in clinical isolates of Klebsiella pneumoniae: a comparison of SDS-PAGE and MALDI-TOF/MS and limitations of whole genome sequencing analysis Porin expression in clinical isolates of Klebsiella pneumoniae: a comparison of SDS-PAGE and MALDI-TOF/MS and limitations of whole genome sequencing analysis
Description	Precise definition of porin profiles is of critical importance to understand the role of porins in antimicrobial resistance. In this study, the outer membrane proteins (OMP) profiles of 26 clinical isolates of Klebsiella pneumoniae and of strain ATCC 13883 (wild-type) and ATCC 700603 (producing SHV-18) have been determined using both sodium-dodecyl-sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption/ionization–time of flight/mass spectrometry (MALDI-TOF/MS). SDS-PAGE was performed using both homemade and commercial gels, and protein bands were identified by liquid chromatography coupled to mass spectrometry. A rapid extraction method was used to analyse OMPs by MALDI-TOF/MS. The sequences of porin genes were obtained by whole genome sequencing (WGS) and mutations were defined by BLAST. Same results were obtained for all strains either using SDS-PAGE or MALDI-TOF/MS. SDS-PAGE showed protein bands of ~35, ~36, and ~37 KDa, identified as OmpA, OmpK36 and OmpK35, respectively. By MALDI-TOF/MS, peaks at ~35700 (OmpA), ~37000 (OmpK35), and ~38000 (OmpK36) m/z were detected. ompK35 was intact in nine wild-type isolates and was truncated in 13 isolates, but OmpK35 was not observed in 3 isolates without mutations in ompK35. One point mutation was detected in another isolate and multiple mutations were detected in the remaining isolate. ompK36 was truncated in two isolates lacking this protein and presented one point mutation (n=1) or multiple mutations in the remaining isolates. In conclusion, MALDI-TOF/MS was reliable for porin detection, but because of the complex regulation of porin genes, WGS cannot always anticipate protein expression, as observed with SDS-PAGE and MALDI-TOF/MS.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_21:34:11.227.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cristina Elías López
SpeciesList	scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: Klebsiella pneumoniae subsp. rhinoscleromatis ATCC 13884; NCBI TaxID: 667127;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF fleX

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-11 04:10:26	ID requested
⏵ 1	2025-05-06 21:34:12	announced

10.1186/s12941-024-00761-9;

El, í, as-L, ó, pez C, Mu, ñ, oz-Rosa M, Guzm, á, n-Puche J, P, é, rez-Nadales E, Chicano-Galvez E, Mart, í, nez-Mart, í, nez L, Porin expression in clinical isolates of Klebsiella pneumoniae: a comparison of SDS-PAGE and MALDI-TOF/MS and limitations of whole genome sequencing analysis. Ann Clin Microbiol Antimicrob, 23(1):103(2024) [pubmed]

submitter keyword: porins,klebsiella, LCMS/MS

Luis Martínez Martínez
contact affiliation	Department of Agricultural Chemistry, Soil sciences and Microbiology, University of Cordoba, Cordoba, Spain.
contact email	luis.martinez.martinez.sspa@juntadeandalucia.es
lab head
Cristina Elías López
contact affiliation	CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
contact email	cristina.elias@imibic.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053879
     1. Label: PRIDE project
     2. Name: Porin expression in clinical isolates of Klebsiella pneumoniae: a comparison of SDS-PAGE and MALDI-TOF/MS and limitations of whole genome sequencing analysis Porin expression in clinical isolates of Klebsiella pneumoniae: a comparison of SDS-PAGE and MALDI-TOF/MS and limitations of whole genome sequencing analysis