Metabolomic profiling of single enlarged lysosomes

Nat Methods. 2021 Jul;18(7):788-798. doi: 10.1038/s41592-021-01182-8. Epub 2021 Jun 14.


Lysosomes are critical for cellular metabolism and are heterogeneously involved in various cellular processes. The ability to measure lysosomal metabolic heterogeneity is essential for understanding their physiological roles. We therefore built a single-lysosome mass spectrometry (SLMS) platform integrating lysosomal patch-clamp recording and induced nano-electrospray ionization (nanoESI)/mass spectrometry (MS) that enables concurrent metabolic and electrophysiological profiling of individual enlarged lysosomes. The accuracy and reliability of this technique were validated by supporting previous findings, such as the transportability of lysosomal cationic amino acids transporters such as PQLC2 and the lysosomal trapping of lysosomotropic, hydrophobic weak base drugs such as lidocaine. We derived metabolites from single lysosomes in various cell types and classified lysosomes into five major subpopulations based on their chemical and biological divergence. Senescence and carcinoma altered metabolic profiles of lysosomes in a type-specific manner. Thus, SLMS can open more avenues for investigating heterogeneous lysosomal metabolic changes during physiological and pathological processes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Transport Systems / metabolism
  • Amino Acid Transport Systems, Basic / genetics
  • Amino Acid Transport Systems, Basic / metabolism
  • Cellular Senescence
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • HEK293 Cells
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Lidocaine / chemistry
  • Lidocaine / metabolism
  • Lysosomes / metabolism*
  • Metabolomics / methods*
  • Patch-Clamp Techniques*
  • Reproducibility of Results
  • Signal-To-Noise Ratio
  • Spectrometry, Mass, Electrospray Ionization / methods*
  • Urinary Bladder Neoplasms / metabolism
  • Urinary Bladder Neoplasms / pathology


  • Amino Acid Transport Systems
  • Amino Acid Transport Systems, Basic
  • SLC66A1 protein, human
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins
  • Lidocaine