Fig. 1
From: A Labrador PeptideAtlas and DIA spectral assay library - resources for proteomics research in dogs
Schematic overview. (a) Preparation of canine tissue, plasma and urine samples followed by mass spectrometry analysis in data-dependent (DDA) and data-independent acquisition (DIA) modes. (b) Data analysis steps to generate a Labrador PeptideAtlas build from DDA data. Raw data were converted, searched with Comet and MSFragger, and further analyzed with the Trans-Proteomic Pipeline including PeptideProphet, iProphet, reSpect and ProteinProphet. (c) DIA spectral assay library generation with Spectronaut, quality control with DIALib-QC, a software tool to evaluate libraries for shortcomings, and sharing of the DIA library through the SWATHAtlas resource. (d) Application of the Labrador DIA library. Analysis of tissue and plasma employing DIA-MS and targeted data extraction with the developed Labrador DIA library.
