Proteomics workflow for APP/Aβ TOMAHAQ analysis in endosomal and lysosomal fractions v1

The ability to detect processing of APP to the Ab amyloid peptide is challenging. This protocols describes methods for analysis of Ab "half-tryptic" peptides from purified organelles (endosomes and lysosomes). The targeted proteomics approach using TOMAHAQ coupled with Tomahto, which is an API for use on a Thermo orbitrap instrument that facilitates detection of trigger peptides and fragmentation of target peptide reporter ions.