Figure 2.

Personalized proteomics pipeline for precision health in ophthalmology: liquid vitreous biopsies can be obtained in the operating room using a vitreous cutter or 23-gauge needle (left). Vitreous samples can be analyzed for protein content using multiplex ELISA arrays (top row). Custom or commercial antibody arrays quantify protein levels in biological samples using fluorescence or chemiluminescence means. Alternatively, vitreous fluid can be analyzed using a mass spectrometry approach (bottom row). Protein mixtures are digested with trypsin (or another digestive protease) and peptides are extracted with organic solvents. Analytes can be enriched using a variety of affinity chromatography techniques. Chromatography (HPLC, UPLC) is used to separate peptides before ionization and mass acquisition by mass spectrometry (e.g., ESI-MS/MS and MALDI-TOF MS/MS). Highly-advanced algorithms (e.g., MASCOT, OMSSA, and X!Tandem) match the thousands of spectra to known protein sequences and proteins quantified either through unlabeled (e.g., spectral counting or DIA) or labeled methods (e.g., MRM/SRM and iTRAQ). Once protein levels are quantified (either from an ELISA or MS experiment), downstream bioinformatics analysis (right) can help put the identified proteins into the context of the disease.