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Cited by 29Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and ApplicationsMetabolomics and Mass Spectrometry Studies

Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics

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Ponnaiyan, Srigayatri, Akter, Fatema, Singh, Jasjot, Winter, Dominic·2020·Scientific Data
DOI 10.1038/s41597-020-0399-5PMC PMC7044164
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Abstract

Lysosomes are the main degradative organelles of cells and involved in a variety of processes including the recycling of macromolecules, storage of compounds, and metabolic signaling. Despite an increasing interest in the proteomic analysis of lysosomes, no systematic study of sample preparation protocols for lysosome enriched fractions has been performed to date. In the current study, we used samples enriched for lysosomes by paramagnetic nanoparticles and systematically evaluated experimental parameters for the analysis of the lysosomal proteome. This includes different approaches for the concentration of lysosome-containing fractions; desalting of samples by solid phase extraction; fractionation of peptide samples; and different gradient lengths for LC-MS/MS analyses of unfractionated samples by data dependent and data independent acquisition. Furthermore, we evaluated four different digestion methods including filter aided sample preparation (FASP), in-gel digestion, and in-solution digestion using either RapiGest or urea. Using the combined data, we generated a benchmark lysosomal proteome data set for mouse embryonic fibroblasts as well as a spectral library for the analysis of lysosomes by data independent acquisition.

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  • Of the 37 GNPTAB trans-CDS pQTLs detected in the collapsing model, 35 (95%) are lysosomal proteins, 18 of which have been associated with other LSDs.

    “Of the 37 GNPTAB trans-CDS pQTLs detected in the collapsing model, 35 (95%) are lysosomal proteins25,26, 18 of which have been associated with other LSDs (Supplementary Table 9).”

    From Rare variant associations with plasma protein levels in the UK Biobank (2023) · cites this paper as [25]

    The Methods (Data processing – DDA) describe a curated lysosomal-protein list, and Technical Validation (Draft map of the MEF lysosomal proteome) reports 740 proteins of known lysosomal origin. This supports using the paper to identify lysosomal proteins, the part to which the citation is attached. The paper does not report GNPTAB pQTLs or establish that 35 of the citing study’s 37 proteins are lysosomal; the 18 associated with other LSDs is attributed to the citing study’s Supplementary Table 9, not this citation. (LLM, conf=0.82)

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Authors
Ponnaiyan, S., Akter, F., Singh, J., & Winter, D.
Affiliations
University of Bonn (DE)
Corresponding author
Winter, Dominic
ORCID
Venue
Scientific Data
Publisher
Springer Science and Business Media LLC
Published
2020-02-26
Volume
7
Issue
1
Pages
68-68
ISSN
2052-4463 (ISSN-L)
DOI
10.1038/s41597-020-0399-5
PMC
PMC7044164
OpenAlex
W3008491580
Cited by
29
References
3
Citations by year
2025: 6 · 2024: 3 · 2023: 3 · 2022: 3 · 2021: 9 · 2020: 5
Type
data paper
Language
en
Open access
Licence
Locations
  • Scientific Data (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National overseas scholarship by Indian Ministry of Social Justice and Empowerment
  • Deutscher Akademischer Austauschdienst
  • Studienstiftung des Deutschen Volkes
  • Deutsche Forschungsgemeinschaft (FOR2625)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
Keywords
lysosomal proteome, mouse embryonic fibroblasts, sample preparation, solid-phase extraction, peptide fractionation, data-dependent acquisition, data-independent acquisition, filter-aided sample preparation, in-gel digestion, in-solution digestion, spectral library
MeSH terms
Animals, Chromatography, Liquid, Embryo, Mammalian, Fibroblasts, Lysosomes, Proteome, Proteomics, Mice, Tandem Mass Spectrometry

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