Table 2

Alteration in the secreted proteome of MRJ(L) expressor of MDA-MB-435

The analysis of secreted proteome was carried out using secreted proteome from MDA-MB-435. Proteins from the conditioned serum-free medium were concentrated using a tC2 reversed-phase sorbent column and digested with trypsin. The resulting peptides were analyzed by electrospray tandem mass spectrometry using a Q-TOF Ultima API-US mass spectrometer equipped with a nanoflow electrospray. The resulting data files were searched using an in-house MASCOT search engine. (MASCOT is a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases [21].) Ion scores higher than 35 (P < 0.05) were considered significant. Only proteins matching at least two peptides in MASCOT were accepted (expectation: AZGP1). MASCOT position indicates (inversely) a relative abundance of the protein in secretome (the lower the score, the higher is the abundance). Matched sequences correspond to the number of nonredundant tryptic peptides mapped to the protein listed under the GenBank accession number. This indicates the confidence with which the protein was identified by mass spectrometry. NCBInr gi#, gene identification number from a comprehensive, nonidentical protein database maintained by National Center for Biotechnology Information. MRJ(L), mammalian relative of DnaJ long isoform.

Mitra et al. Breast Cancer Research 2008 10:R22   doi:10.1186/bcr1874