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PXD014576

PXD014576 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleComprehensive proteomic analysis of mouse embryonic fibroblast lysosomes by mass spectrometry
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:03:20.491.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterJasjot Singh
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationListS-carboxamidoethyl-L-cysteine
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-07-11 07:59:11ID requested
12020-02-18 10:46:00announced
22024-10-22 04:03:21announced2024-10-22: Updated project metadata.
Publication List
Dataset with its publication pending
Keyword List
curator keyword: Biological
submitter keyword: LC-MSMS, DIA,Lysosome
Contact List
Dominic Winter
contact affiliationInstitute for Biochemistry and Molecular Biology, University of Bonn,Germany.
contact emaildominic.winter@uni-bonn.de
lab head
Jasjot Singh
contact affiliationUniversity of Bonn
contact emailjasjotsingh@web.de
dataset submitter
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Dataset FTP location
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PRIDE project URI
Repository Record List
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