PXD047792

PXD047792 is an original dataset announced via ProteomeXchange.

Title	Mass-spectrometry-based genetic analysis of lysosome-related organelle in the intestine of Caenorhabditis elegans
Description	The nematode intestine is the primary site for nutrient uptake and storage as well as the synthesis of important molecules; parts of its functions rely on a type of lysosome-related organelle known as gut granules. However, aspects of the intestine are not well understood, including the exporting of its molecules and that of the gut granules, in which only a few of the organelle’s protein content is identified. Here, we report a mass-spectrometry-based proteomic analysis of the intestine of the Caenorhabditis elegans and of these lysosome-related organelles. We identified around 5000 proteins each in the intestine and the gonad and showed that most of these proteins can be identified using samples extracted from a single worm, suggesting the feasibility of individual-level proteomic-based genetics analysis. Comparing the proteome to that of the transcriptome, we identify proteins that may be synthesized in the intestine and transferred to the gonad. To identify gut granule proteins, we compared the intestinal proteome of individual intestines that largely lack gut granules to that of the wild-type. The identified gut granule proteome includes proteins previously known to be exclusively localized to the granules, and we validated two more with immunohistochemistry analysis, including a worm ortholog of the mammalian ABCC6/MRP6, suggesting that our strategy was effective in identifying the gut granule proteome. Our results demonstrate the practicability of single tissue mass-spectrometry-based proteomic analyses in small organisms such as nematodes, as well as its utility for making discoveries in a previously prohibitive area.
HostingRepository	PRIDE
AnnounceDate	2025-01-06
AnnouncementXML	Submission_2025-01-06_13:39:19.335.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ting-Yu Wang
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-13 06:34:49	ID requested
1	2024-05-23 11:00:54	announced
2	2024-10-22 06:42:02	announced	2024-10-22: Updated project metadata.
⏵ 3	2025-01-06 13:39:19	announced	2025-01-06: Updated project metadata.

Dataset with its publication pending

submitter keyword: Adult,Intestine, glo-1, lysosome-related organelle, Gonad

Tsui-Fen Chou
contact affiliation	Division of Biology and Biological Engineering, California Institute of Technology
contact email	tfchou@caltech.edu
lab head
Ting-Yu Wang
contact affiliation	Caltech
contact email	tywang@caltech.edu
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/2024/05/PXD047792

PRIDE project URI

• PRIDE
  1. PXD047792
     1. Label: PRIDE project
     2. Name: Mass-spectrometry-based genetic analysis of lysosome-related organelle in the intestine of Caenorhabditis elegans