MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery: application to lens development and cataract

Hum Genet. 2020 Feb;139(2):151-184. doi: 10.1007/s00439-019-02095-5. Epub 2019 Dec 3.


While the bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery) effectively identifies human cataract-associated genes, it is currently based on just transcriptome data, and thus, it is necessary to include protein-level information to gain greater confidence in gene prioritization. Here, we expand iSyTE through development of a novel proteome-based resource on the lens and demonstrate its utility in cataract gene discovery. We applied high-throughput tandem mass spectrometry (MS/MS) to generate a global protein expression profile of mouse lens at embryonic day (E)14.5, which identified 2371 lens-expressed proteins. A major challenge of high-throughput expression profiling is identification of high-priority candidates among the thousands of expressed proteins. To address this problem, we generated new MS/MS proteome data on mouse whole embryonic body (WB). WB proteome was then used as a reference dataset for performing "in silico WB-subtraction" comparative analysis with the lens proteome, which effectively identified 422 proteins with lens-enriched expression at ≥ 2.5 average spectral counts, ≥ 2.0 fold enrichment (FDR < 0.01) cut-off. These top 20% candidates represent a rich pool of high-priority proteins in the lens including known human cataract-linked genes and many new potential regulators of lens development and homeostasis. This rich information is made publicly accessible through iSyTE (, which enables user-friendly visualization of promising candidates, thus making iSyTE a comprehensive tool for cataract gene discovery.

MeSH terms

  • Animals
  • Biomarkers / metabolism*
  • Cataract / genetics
  • Cataract / metabolism*
  • Cataract / pathology
  • Computational Biology
  • Computer Simulation*
  • Eye Proteins / genetics
  • Eye Proteins / metabolism*
  • Gene Expression Profiling
  • Humans
  • Lens, Crystalline / embryology
  • Lens, Crystalline / metabolism*
  • Mice
  • Mice, Inbred C57BL
  • Proteome / analysis
  • Proteome / metabolism*
  • Tandem Mass Spectrometry / methods*
  • Transcriptome


  • Biomarkers
  • Eye Proteins
  • Proteome