Computational protocol: Data from a proteomic analysis of colonic fibroblasts secretomes

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Protocol publication

[…] Secreted proteins were extracted from the conditioned medium of one pair of the fibroblast cultures. We performed a proteomic analysis of the proteins using a Synapt G1 mass spectrometer. The mass data interpretation was performed using ProteinLynx Global Server, X! Tandem and Scaffold softwares. The proteomic data presented here include the protein and spectrum identification results, as well as the cellular component annotation and functional analyzing results. 227 proteins were identified with a false discovery rate of 1.3% based on 15,000 assigned spectra. Half of the proteins were novel identifications in the secretome of colonic fibroblasts comparing with the known report. The subcellular localization of the identified proteins were annotated using UniProt database, DAVID, SignalP, SecretomeP, Phobius, WoLF PSORT and exosome databases. The occurrence of the fibroblast secretome proteins in the colon cancer cell proteomes was also analyzed. The functional enrichment of the identified proteins was performed using DAVID. […]

Pipeline specifications

Software tools PLGS, X! Tandem, DAVID, SignalP, SecretomeP, Phobius, WoLF PSORT
Applications MS-based untargeted proteomics, Protein sequence analysis
Diseases Colonic Neoplasms, Neoplasms, Colorectal Neoplasms