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GPM-MRM is functionality that has been added to The GPM to assist researchers in finding signature combinations of peaks in MS/MS spectra. Spectra can be searched by mass, accession number of peptide sequence, and the results can be pared down by fragment mass presence or uniqueness.

Types of Searches

The default values for some of the search parameters are as follows:

  • parent ion mass range: 0.1 kDa
  • fragment ion mass range: 0.1 kDa
  • peak sorting: mass, increasing

A search can be performed with one of the following sets of data:

  • parent ion mass
    • returns all spectra within the given range
  • sequence
    • returns all spectra applying to that peptide sequence.
    • For finding unique peaks, peaks for that sequence are compared against other spectra within range of all observed weights of that sequence.
  • accession number
    • Returns the list of peptides that have been identified for a given accession number

For any of the above searches, providing the fragment ion mass will mask out results that did not include a fragment ion within the given range of the supplied fragment ion mass.

The fragment ion mass range is used to classify fragment masses as unique or not. In a result set, and two masses between different results within the fragment ion mass range are considered to be the same, and therefore non-unique. A larger fragment ion mass range will lead to fewer fragment ions being considered unique.

Search Results

The data returned by the search returns in the following order:

  • Sequence: the residue sequence of the peptides.
  • m/z: the mass-to-charge ratio recorded
  • z: the charge
  • Accession #'s: the list of identified proteins in which this peptide has been identified
  • Peaks: up to 20 mass/intensity peaks from the spectra

Unique fragment ion masses are colour-coded for fast identification, and the rows of results are ordered from fewest to most corresponding accession numbers. The peak/intensity tables can be displayed either by ascending weight or descending intensity. Non-unique peaks can be masked out for a simplified display.

Example Searches

The links below demonstrate the different search and display parameters.

  • Peptide sequence WIYEDVER
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