Computational protocol: Secreted Giardia intestinalis cysteine proteases disrupt intestinal epithelial cell junctional complexes and degrade chemokines

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Protocol publication

[…] Proteomics was performed essentially as described earlier []. Proteins were reduced, alkylated and in-gel digested by trypsin, dried and resolved in 15 μL 0.1% FA (formic acid). Peptides were separated in reversed-phase on a C18-column and electrosprayed on-line to an LTQ Orbitrap Velos Pro ETD mass spectrometer (Thermo Finnigan). Tandem mass spectrometry was performed applying CID and it was performed at proteomics core facility at SciLifelab, Uppsala, Sweden.Database searches were performed using the Sequest algorithm, embedded in Proteome Discoverer 1.4 (Thermo Fisher Scientific), towards a FASTA database containing proteins from Giardia, downloaded from giardiadb.org/common/downloads/release5.0/GintestinalisAssemblageA/. The search criteria for protein identification were set to at least one matching peptide of 95% confidence level per protein. In addition, database searches against human proteins in Swissprot were performed in order to identify possible contaminations. […]

Pipeline specifications

Software tools Comet, Proteome Discoverer
Databases GiardiaDB
Application MS-based untargeted proteomics
Organisms Giardia intestinalis, Komagataella pastoris
Diseases Dysentery, Giardiasis, Infection
Chemicals Cysteine