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.