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Peptide mass fingerprinting
Peptide Mapping

or Peptide mass fingerprinting (PMF) is a protein identification technique in which SAI's MALDI MS can be used to measure the masses of proteolytic peptide fragments. The protein is then identified by matching the measured masses to corresponding peptide masses from protein or nucleotide sequence databases. Peptide mass fingerprinting works well for analytical proteomics because it combines a conceptually simple approach with robust, high throughput instrumentation such as SAI's  LaserToF MALDI range. As with other MS based analytical proteomics techniques, the quality of the protein identifications  depends on the quality of the MS data itself, the accuracy of the databases, and the power of the search algorithms and software used.

Fortunately for the user, SAI can offer all three of the ingredients for success in this approach to proteomics


In MS-MS mode, a peptide ion is isolated in the mass analyzer and subjected to downstream dissociation to produce product ion fragments. The amino acid sequence of the original precursor ion can be deduced from the masses of the fragment ions; this forms the basis for de novo sequencing by MS-MS. Fragmentation data can be used to determine a short stretch of amino acid sequence (a "sequence tag"), which can be used to search a database. A more convenient approach is to compare product ion spectra directly with databases to identify the intact protein.  SAI’s linear-reflectron ToF-ToF mass spectrometers LT3 and TT  are specifically designed to offer  post source decay (PSD) (and for the TT only, collision induced dissociation, CID) methods, achieving accurate seamless single scan MS-MS data in the most efficient way possible.

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