Collecting and sequencing proteins

Since ProteinTrawler records the retention time of each protein mass, it is a simple endeavor to maintain chromatographic conditions, split the flow that exits the LC column with a small portion set to the mass spectrometer to monitor for assurance that there were no changes in the retention time that would hinder the pooling of fractions from multiple runs, and to facilitate the determination of which fractions contained the desired proteins. In our experimental setup, the flow was split after the column with 25% of the flow going to the mass spectrometer while the remaining diverted to an HP1100 fraction collector. The fraction collector was used to collect fractions at 1.0-minute intervals. 

The PepSeq program of Micromass s ProteinLynx software package was used for de novo analysis of the sequence (MS/MS) data. MS-Pattern of ProteinProspectror55 used the sequence tag determined from PepSeq to search the nonredundant database of the National Center for Biotechnology Information (NCBI) for protein identification. 

1 Salmonella enterica Serovar Newport Isolated from Different Animals 

Because the genome of E. sakazakii has not yet been sequenced and deposited into the National Center for Biotechnology Information (NCBI) 

Strain Lab ID Devalue (seconds) 29,563 Da protein Hypothetical protein Mflag020121 

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