PXD057536-1

PXD057536 is an original dataset announced via ProteomeXchange.

Title	Cell type-specific in vivo proteomes with a multicopy mutant methionyl tRNA synthetase mouse line
Description	The functional diversity of cells is driven by the different proteins they express. While improvements in protein labeling techniques have enabled the measurement of proteomes with increased sensitivity, measuring cell type-specific proteomes in vivo remains challenging. One of the most useful pipelines is bio-orthogonal noncanonical amino acid tagging (BONCAT) with the MetRS* system, consisting of a transgenic mouse line expressing a mutant methionyl-tRNA synthetase (MetRS*) controlled by Cre recombinase expression. This system allows cell type-specific labeling of proteins with a noncanonical amino acid (azidonorleucine, ANL), which can be subsequently conjugated to affinity or fluorescent tags using click chemistry. Click-modified proteins can then be visualized, purified and identified. The reduction in sample complexity enables the detection of small changes in protein composition. Here, we describe a multicopy MetRS* mouse line (3xMetRS* mouse line) that exhibits markedly enhanced ANL protein labeling, boosting the sensitivity and temporal resolution of the system and eliminating the need for working under methionine depletion conditions. Cell type-specific in vivo labeling is possible even in heterozygous animals, thus offering an enormous advantage for crossing the line into mutation and disease-specific backgrounds. Using the 3xMetRS* line, we identified the in vivo proteome of a sparse cell population - the dopaminergic neurons of the olfactory bulb - and furthermore determined newly synthesized proteins after short labeling durations following a single intraperitoneal ANL injection.
HostingRepository	PRIDE
AnnounceDate	2025-08-28
AnnouncementXML	Submission_2025-08-28_07:12:27.728.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julian Langer
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-05 06:22:28	ID requested
⏵ 1	2025-08-28 07:12:28	announced

Alvarez-Pardo R, Tom Dieck S, Desch K, Nassim Assir B, Olmedo Salinas C, Sivakumar RS, Langer JD, Schuman EM, Alvarez-Castelao B, Cell type-specific in vivo proteomes with a multicopy mutant methionyl tRNA synthetase mouse line. Lab Anim (NY), 54(9):228-237(2025) [pubmed]

10.1038/s41684-025-01589-2;

submitter keyword: in vivo, excitatory neurons, cortex,cell-type specificity, click chemistry, protein synthesis, nascent proteome, ANL, BONCAT, metabolic label, low input, olfactory bulb, dopaminergic neurons

Julian D.
contact affiliation	Max Planck Institute for Brain Research 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/2025/08/PXD057536

PRIDE project URI

• PRIDE
  1. PXD057536
     1. Label: PRIDE project
     2. Name: Cell type-specific in vivo proteomes with a multicopy mutant methionyl tRNA synthetase mouse line