Sequencing of novel protein from Bacillus pumilus PH-01 using a high-resolution hybrid quadrupole-time-of-flight mass spectrometer

Protein identification can be accomplished with an enzymatic digestion of the protein followed by mass spectrometric analysis of the peptide mass fingerprint followed by database searching. However, if a protein is not in a database, sequence information must be obtained to characterize and identify it. This can be done either by classical Edman sequencing or/and by tandem mass spectrometry. To determine the sequence of an unknown protein from Bacillus pumilus PH-01, which adsorbs environmental pollutants such as polychlorinated dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and biphenyls (PCBs), both sequencing and de novo peptide sequencing by tandem MS/MS of the peptide fragments were performed. Edman sequencing of the reduced and alkylated protein revealed the majority of the sequence; however, all information on disulfide bonding was lost. Therefore, a tryptic digest of the native protein was performed to obtain both complete sequence information and the connectivity of the disulfide bonds. We performed the de novo sequencing using a hybrid quadrupole-time-of-flight mass spectrometer (Q-TOF MS) instrument. The high mass accuracy and sensitivity of the hybrid Q-TOF MS made low-level sequencing of this novel naturally isolated protein possible. (C) 2001 Elsevier Science B.V.