Spectrum, peptide mass fingerprint

Fig. 4. Mascot search results summary page using peptide mass fingerprint (PMF) data from the spectrum in Fig. 1.

Figure 1 5 MALDI spectrum from a 2-D gel spot excised from a human proteomic study in which the corresponding spectrum of the cathepsin D precursor could be identified after using SMEC micropreparation sample preparation followed by elution and spotting onto the MALDI target plate and MALDI analysis. The peptide mass fingerprinting revealed the identity of the protein using the Mascot bioinformatic software and the Swissprot protein database. The ( ) indicates the peptide masses corresponding to the cathepsin D precursor, and (T) the trypsin peptide fragments that were used for internal mass calibration.

Figure 3. Identification of a protein by peptide mass fingerprinting. The protein constituents of pig saiiva were separated by SD-PAGE and a protein band was digested with trypsin. The resuitant tryptic peptides were mass-measured using MALDI-ToF mass spectrometry. The peptides in the mass spectrum were either derived from trypsin self-digestion (T) or were derived from the protein in the gel- Database searching with the masses of these peptides led to an unequivocal identification of the protein as SAL (salivary lipocalin). The inset map shows the theoretical tryptic digestion map of this protein, and underneath are the peptides that were observed. In many instances, smaller peptides were visible as partial digestion products.

Figure 4 Peptide mass fingerprints of recombinant proteins (EPR) used in doping MALDITOF-MS spectrum of (A) Glu-C digested EPR and (B) Glu-C digested and deglycosylated EPR. (Reprinted with permission from Stanley and Poljak (2003) Journal of Chromatography B 1 5-. 205-218 Elsevier.)...

As mentioned above, MALDI oa-TOF-MS is feasible and the hybrid quadrupole TOF systems are available to provide the additional feature of MS/ MS. One of the key advantages of MALDI TOF-MS is that it can provide a simple spectrum that reveals the molecular ions from a complex mixture. This is a common experiment in protein analysis, where a list of peptide masses that is referred to as a peptide mass fingerprint (PMF) is generated after digestion of an isolated whole protein with a proteolytic reagent (see Figure 4). The PMF is compared to databases of... 

Then the mass spectrum of the mentioned peptide mixture is measured. The set of molecular mass values (peak list) corresponding to individual peptides is characteristic for the protein and can be considered as its fingerprint. 

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