PXD014576

PXD014576 is an original dataset announced via ProteomeXchange.

Title	Comprehensive proteomic analysis of mouse embryonic fibroblast lysosomes by mass spectrometry
Description	The lysosome is the main degradative organelle in eukaryotic cells. It is involved in diverse cellular functions from intracellular digestion to metabolic signaling. Despite various efforts to enrich for lysosomes and analyze their proteome with mass spectrometry based proteomics approaches, no systematic evaluation of sample preparation parameters for the analysis of lysosome enriched fractions has been performed. Using samples enriched for lysosomes with paramagnetic nanoparticles, we conducted a systematic evaluation of the protocol for the analysis of the lysosomal proteome. We compared centrifugation and protein precipitation for the concentration of lysosome enriched fractions and tested four different digestion methods in combination with each of these approaches. This included filter aided sample preparation (FASP), in-gel digestion, and in solution digestion using either RapiGest or Urea. Furthermore, we evaluated three formats for sample desalting, four gradient lengths for LC-MSMS analysis of unfractionated samples, as well as fractionation by strong anion exchange tip columns into three or six fractions. Using the combined data, we generated a draft map of lysosomal proteome for mouse embryonic fibroblasts as well as a spectral library for the analysis of lysosomes by data independent acquisition (DIA) and evaluated different LC gradient lengths for DIA.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:03:20.491.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jasjot Singh
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	S-carboxamidoethyl-L-cysteine
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-11 07:59:11	ID requested
1	2020-02-18 10:46:00	announced
⏵ 2	2024-10-22 04:03:21	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: LC-MSMS, DIA,Lysosome

Dominic Winter
contact affiliation	Institute for Biochemistry and Molecular Biology, University of Bonn,Germany.
contact email	dominic.winter@uni-bonn.de
lab head
Jasjot Singh
contact affiliation	University of Bonn
contact email	jasjotsingh@web.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD014576
     1. Label: PRIDE project
     2. Name: Comprehensive proteomic analysis of mouse embryonic fibroblast lysosomes by mass spectrometry