PXD058422-1

PXD058422 is an original dataset announced via ProteomeXchange.

Title	Detection and quantitation of small proteins using mass spectrometry
Description	Small proteins or microproteins, despite long being ignored, have important roles in the regulation of larger protein complexes, metabolic pathways and gene expression. However, these proteins remain underrepresented in proteomics studies due to low detection efficiency in traditional mass spectrometry workflows. Their inherent characteristics often lead to depletion during sample preparation and a low detection efficiency in liquid chromatography-mass spectrometry (LC-MS). To improve detection and quantitation, we took advantage of the large set of documented small proteins in Escherichia coli and systematically compared and optimized different sample preparation and LC-MS approaches. We evaluated different top-down and bottom-up approaches, including data-dependent acquisition (DDA), data-independent acquisition (DIA) and parallel reaction monitoring (PRM). Our data highlight the benefit of top-down proteomics for identifying new small proteins and bottom-up preparation coupled with PRM acquisition for quantitation of protein levels in different growth conditions. Our systematic comparison can serve as a guideline for MS detection of small proteins in all organisms.
HostingRepository	PRIDE
AnnounceDate	2025-09-03
AnnouncementXML	Submission_2025-09-03_14:58:14.424.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julian Langer
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; monohydroxylated residue; formylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-29 11:37:12	ID requested
⏵ 1	2025-09-03 14:58:15	announced

Franco PHC, Zeinert R, Meier-Credo J, Storz G, Langer JD, Detection and Quantitation of Small Proteins Using Mass Spectrometry. Mol Cell Proteomics, 24(9):101052(2025) [pubmed]

10.1016/j.mcpro.2025.101052;

submitter keyword: orbitrap eclipse,proteomics, PRM, top-down, escherichia coli

Julian D.
contact affiliation	Max Planck Institute of Biophysics
contact email	julian.langer@biophys.mpg.de
lab head
Julian Langer
contact affiliation	MPIs for Biophysics and Brain Research
contact email	julian.langer@biophys.mpg.de
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/2025/09/PXD058422

PRIDE project URI

• PRIDE
  1. PXD058422
     1. Label: PRIDE project
     2. Name: Detection and quantitation of small proteins using mass spectrometry