Computational protocol: Partial Characterization of Venom from the Colombian Spider Phoneutria Boliviensis (Aranae:Ctenidae)

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Protocol publication

[…] Ten micrograms of sample (two well-defined and significant peaks eluting at 48 and 53 min) were reduced with 100 mM DTT, alkylated with 100 mM iodoacetamide and then trypsinized. Digestion was allowed to proceed for 16 h at 30 °C. Protein identification was performed by HPLC-nESI-MS/MS on a C18 nano-column using a 1200 Agilent chromatograph coupled to a 6310 IonTrap mass spectrometer (Agilent). Resulting spectra were analyzed using Spectrum Mill (Agilent Technologies, Santa Clara, CA, USA) and Mascot (MatrixScience, Boston, MA, USA) in the NCBInr protein databases, with carbamidomethylation as fixed modification. Peptide sequences were searched for similarity using BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) and the Arachnoserver database [,] (http://www.arachnoserver.org/mainMenu.html), and aligned with related arachnid peptides using ClustalW []. […]

Pipeline specifications

Software tools Spectrum Mill, Clustal W
Databases ArachnoServer
Application MS-based untargeted proteomics
Organisms Canine mastadenovirus A
Chemicals Calcium, N-Methylaspartate, Glutamic Acid