PXD014576 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
Dataset with its publication pending |
Keyword List
curator keyword: Biological |
submitter keyword: LC-MSMS, DIA,Lysosome |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD014576
- Label: PRIDE project
- Name: Comprehensive proteomic analysis of mouse embryonic fibroblast lysosomes by mass spectrometry