PXD058426-1

PXD058426 is an original dataset announced via ProteomeXchange.

Title	Nanochip proteome of Klebsiella
Description	In this study, we used an interdisciplinary approach, combining biophysics and systems biology, to design a microfluidic chip for the multiplexed detection and separation of pathogen cells from immune cells combined with proteomic profiling using mass spectrometry. Our nanochip design includes precise control of the microfabricated filters pore size for exclusion of cell types based on size to reliably separate bacteria from immune cells (REF 20, 21 NFRF), enabling separation of the pathogen into distinct populations. Our results show consistency in macrophage cell proteomes using a traditional ‘cell scraping’ vs. nanochip collection of host cells, demonstrating minimal disruption to the infectome profile. However, comparison between ‘cell scraping proteome profiling and nanochip proteome profiling reveals deeper coverage of the bacterial proteome, a key component when investigating regulators of bacterial virulence. Additionally, separation of K. pneumoniae cells into non-phagocytosed vs. phagocytosed (or associated) distinct populations provides new biological insights into mechanisms of immune cell evasion used by the bacterium to promote survival within the host . This information presents a plethora of new targets for inhibition or perturbation to weaken the bacterium and enhance clearance by the host. Here, we present a reproducible and adaptable technological platform that combines the precision of microfluidics with the power of mass spectrometry-based proteomics to distinguish biological systems and to delve deeper into mechanisms regulating the outcome of infectious disease.
HostingRepository	PRIDE
AnnounceDate	2026-03-21
AnnouncementXML	Submission_2026-03-21_13:46:56.527.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jennifer Geddes-McAlister
SpeciesList	scientific name: Klebsiella pneumoniae subsp. pneumoniae; NCBI TaxID: NEWT:72407;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-29 14:34:11	ID requested
⏵ 1	2026-03-21 13:46:57	announced

Dataset with its publication pending

submitter keyword: Quantitative proteomics, microfluidics, Klebsiella pneumoniae, nanochip technology, macrophages, anti-virulence, systems biology

Jennifer Geddes-McAlister
contact affiliation	University of Guelph 50 Stone Rd E Guelph, ON, Canada
contact email	jgeddesm@uoguelph.ca
lab head
Jennifer Geddes-McAlister
contact affiliation	University of Guelph
contact email	jgeddesm@uoguelph.ca
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/2026/03/PXD058426

PRIDE project URI

• PRIDE
  1. PXD058426
     1. Label: PRIDE project
     2. Name: Nanochip proteome of Klebsiella