ArticleProteomes2021
Targeted Quantification of the Lysosomal Proteome in Complex Samples.
Article in Proteomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Label-Free Targeted Proteomics Data Analysis Workflow Selection - Benchmarking AI-based and Data-Driven Approaches.Molecular & cellular proteomics : MCP · 2026Article
- Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.Nature cell biology · 2026Article
- Benchmarking Lysosome Enrichment Methods: A Guide for Research and Clinical Translation.Analytical chemistry · 2026Article
- Mass Spectrometry-Based Proteomic Analysis of Lysosome-Enriched Fractions.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Proteomics Insights Into Lysosome Biogenesis and Maturation.Proteomics · 2025Review
- The V-ATPase complex component RNAseK is required for lysosomal hydrolase delivery and autophagosome degradation.Nature communications · 2024Article
- Interrogating data-independent acquisition LC-MS/MS for affinity proteomics.Journal of proteins and proteomics · 2024Article
- A Mouse Systems Genetics Approach Reveals Common and Uncommon Genetic Modifiers of Hepatic Lysosomal Enzyme Activities and Glycosphingolipids.International journal of molecular sciences · 2023Article
- The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection.Science (New York, N.Y.) · 2022Article
- Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics.Journal of proteome research · 2022Article
- Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis.Molecular metabolism · 2022Review
- Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research.Molecules (Basel, Switzerland) · 2022Review
- Proteomic Analysis of Trichomonas vaginalis Phagolysosome, Lysosomal Targeting, and Unconventional Secretion of Cysteine Peptidases.Molecular & cellular proteomics : MCP · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
In eukaryotic cells, lysosomes play a crucial role in the breakdown of a variety of components ranging from small molecules to complex structures, ascertaining the continuous turnover of cellular building blocks. Furthermore, they act as a regulatory hub for metabolism, being crucially involved in the regulation of major signaling pathways. Currently, ~450 lysosomal proteins can be reproducibly identified in a single cell line by mass spectrometry, most of which are low-abundant, restricting their unbiased proteomic analysis to lysosome-enriched fractions. In the current study, we applied two strategies for the targeted investigation of the lysosomal proteome in complex samples: data-independent acquisition (DIA) and parallel reaction monitoring (PRM). Using a lysosome-enriched fraction, mouse embryonic fibroblast whole cell lysate, and mouse liver whole tissue lysate, we investigated the capabilities of DIA and PRM to investigate the lysosomal proteome. While both approaches identified and quantified lysosomal proteins in all sample types, and their data largely correlated, DIA identified on average more proteins, especially for lower complex samples and longer chromatographic gradients. For the highly complex tissue sample and shorter gradients, however, PRM delivered a better performance regarding both identification and quantification of lysosomal proteins. All data are available via ProteomeXchange with identifier PXDD023278.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.