Computational identification and functional annotation of tomato wilt pathogen (Fusarium oxysporum f. sp. lycopersici) CAZymes in xylem sap proteome

The LTQ Orbitrap label-free mass spectrometric data of tomato xylem sap with accession: PXD011072 was downloaded from publically available proteomic database PRIDE and analyzed on MaxQuant version 1.6.17.0 (Tyanova et al. 2016a) for protein identification using an inbuilt search engine against the protein database created by taking Fusarium oxysporum f. sp. lycopersici (Fol) and tomato proteins with an in-built contaminant database (246 proteins). Label-free quantification was done using default parameters (Cox et al. 2011, 2014) with a match between runs enabled and label-free quantification (LFQ) minimum ratio count set to 1. An extra variable modification- deamidation (NQ) was also included to quantify the peptides/proteins.