Peak Detection and Spectrum Intensity Images

The purpose of the molecular scanner is for the identification of proteins that were separated with a 2-DE gel. Therefore, for each scan point, the lists of peptide masses are submitted to the peptide mass fingerprint identification program Smartldent [51], which searches the protein sequence database SWISS-PROT and returns a list of matching proteins and their score. 

The resolution power of a 2-DE gel is limited, and therefore several proteins may be found in the same position in a gel [184]. In MALDl MS, the presence of one peptide can attenuate the signal of another and some peptides are difficult to detect [80], resulting in a limited number of peptides per protein expressed in the spectrum. Eor the E. coli and human plasma scan the protein concentration on the PVDF membrane was low and we had to set the minimal number of matching peptide masses to 3 in order to identify some weekly expressed proteins. The mass tolerance was set to a value as high as 0.6 Dalton due to cahbration errors and one missed cleavage was accepted. 

Peak lists and identification results are then written into a text file. The 2-DE gel analysis tool Melanie [148] can read this file and allows loading the molecular scanner data for visualisation. It allows selecting scan points and viewing the identification results and spectra of these points. 

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