PXD077117

PXD077117 is an original dataset announced via ProteomeXchange.

Title	Pushing the limits of SCP: bacSCP, a proof-of-concept study to investigate heterogeneity of bacteria by single cell proteomics.
Description	Single-cell proteomics (SCP) has emerged as a powerful approach to quantify protein expression variability at cellular resolution, yet most state-of-the-art workflows are tailored to eukaryotic cells with only one study exploring how single bacteria can be analyzed by mass spectrometry. Here, we established bacSCP, a protocol extending SCP to bacterial cells, facing analytical challenges such as the thick bacterial cell wall hampering lysis, the extremely small cell size and resultant low protein content, and the consequently relatively high level of contaminating proteins from external sources. Using this bacSCP pipeline, we quantified more than 50 bacterial proteins from single Bacillus subtilis and Escherichia coli cells. Upon heat stress, we reproducibly observed up to 8-fold upregulation of chaperones including GroEL, GroES, and ClpC for a B. subtilis mcsB strain. Importantly, single-cell measurements revealed potential heterogeneity within the heat-stressed subpopulation, enabling interrogation of stress-response variability at the proteome level. These results demonstrate the feasibility of bacSCP and provide a foundation for studying bacterial stress adaptation and phenotypic diversity with single-cell proteomic resolution.
HostingRepository	PRIDE
AnnounceDate	2026-08-04
AnnouncementXML	Submission_2026-08-04_08:07:33.103.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Matzinger
SpeciesList	scientific name: Bacillus subtilis TPK 210909; NCBI TaxID: NEWT:1077281; scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	quadrupole orbitrap astral instrument

Revision	Datetime	Status	ChangeLog Entry
0	2026-04-14 00:04:46	ID requested
⏵ 1	2026-08-04 08:07:33	announced

Dataset with its publication pending

submitter keyword: liquid chromatography, heat shock response, mass spectrometry,single-cell proteomics, single bacteria proteomics

Karl Mechtler
contact affiliation	Research Institute of Molecular Pathology, Campus Vienna Biocenter, 1030 Vienna, Austria
contact email	karl.mechtler@imp.ac.at
lab head
Manuel Matzinger
contact affiliation	IMP / University of Vienna
contact email	manuel.matzinger@imp.ac.at
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/2026/08/PXD077117

PRIDE project URI

• PRIDE
  1. PXD077117
     1. Label: PRIDE project
     2. Name: Pushing the limits of SCP: bacSCP, a proof-of-concept study to investigate heterogeneity of bacteria by single cell proteomics.