GPM-MRM

Revision as of 17:38, 10 April 2008

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 any combination of parent ion mass, accession number or 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 any combination of the following parameters:

• 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

The order of precedence in searching is mass, residue sequence, accession number. If more than one of those parameters is provided, the lower priority parameters will be used to filter results that contain only that parameter.

For any of the above searches, providing the fragment ion mass will filter 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 (changeable parameters show in bold):

• Peptide sequence WIYEDVER: Results
• Parent ion mass 1735 kDa, parent mass range of 1.0 kDa: Results
• Same as above, but show only results with accession number ENSP00000350063: Results
• Parent ion mass 889 kDa, parent mass range of 0.5 kDa, fragment ion range of 1.0 kDa, filtered by sequence AMGIMNSFVNDIFER and accession number IPI00419833.7, peaks ordered by intensity with only unique peaks shown: Results

References

• Multiple Reaction Monitoring as a Method for Identifying Protein Posttranslational Modifications : Abstract