Computational protocol: Identification of Human Tissue Kallikrein 6 as a Potential Marker of Laryngeal Cancer Based on the Relevant Secretory/Releasing Protein Database

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Protocol publication

[…] ProteinLynx GlobalServer version 2.3 (Waters, MA, USA) was used to create peak list files. Database searches were performed with the pFind 2.4 search engine (http://pfind.ict.ac.cn/) against Uniprot Knowledgebase Release 12.6 (human, 76137 entries). The search criteria for the peptide and protein identification were reported previously []. In brief, two missed cleavages were allowed, carbamidomethylation (Cys) was set as a fixed modification, oxidation (Met) was set as a variable modifications, precursor ion mass tolerance was 0.2 Da, fragments ion mass tolerance was set to 0.3 Da, and FDR was set as 1% by default. The substantial properties of the CM protein database were broadly analyzed with the BiNGO tool []. […]

Pipeline specifications

Software tools pFind, BiNGO
Databases UniProtKB
Application MS-based untargeted proteomics
Organisms Homo sapiens
Diseases Neoplasms
Chemicals Kallikreins