(→Types of Searches) |
(→Types of Searches) |
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* parent ion mass range: 0.1 kDa | * parent ion mass range: 0.1 kDa | ||
* fragment ion mass range: 0.1 kDa | * fragment ion mass range: 0.1 kDa | ||
- | * peak sorting: | + | * peak sorting: intensity, decreasing |
A search can be performed with any combination of the following parameters: | A search can be performed with any combination of the following parameters: | ||
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*accession number | *accession number | ||
**when used in combination with sequence or parent ion mass, specifying the accession number acts as a filter, displaying only those results which both meet the mass or sequence criteria '''and''' were found for the given protein. | **when used in combination with sequence or parent ion mass, specifying the accession number acts as a filter, displaying only those results which both meet the mass or sequence criteria '''and''' were found for the given protein. | ||
- | **when used alone, it returns a summary page of eleven columns. By default, the columns are sorted in order of the number of GPMDB entries for a peptide in z=2 | + | **when used alone, it returns a summary page of eleven columns. By default, the columns are sorted in order of the number of GPMDB entries for a peptide in z=2 charge state. A dash ('''—''') in the table represents zero. |
- | + | ||
**#'''Peptide Sequence''': the peptides sequence identified | **#'''Peptide Sequence''': the peptides sequence identified | ||
**#'''Charge''': charge states observed for this peptide in this protein | **#'''Charge''': charge states observed for this peptide in this protein | ||
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**#'''MRMs''': the number of spectra used to calculate the information stored in the peakdb tables for this peptide. | **#'''MRMs''': the number of spectra used to calculate the information stored in the peakdb tables for this peptide. | ||
**#'''Observed z=1''': the number of identifications of this peptide stored in GPMDB with charge state 1. | **#'''Observed z=1''': the number of identifications of this peptide stored in GPMDB with charge state 1. | ||
- | **#'''Observed z=2 | + | **#'''Observed z=2''': the number of identifications of this peptide stored in GPMDB with charge state 2. |
+ | **#'''Observed z=3''': the number of identifications of this peptide stored in GPMDB with charge state 3. | ||
**#'''log<sub>10</sub>(ω/ω<sub>0</sub>) z=1''': the normalized peptide count for this peptide in charge state 1. | **#'''log<sub>10</sub>(ω/ω<sub>0</sub>) z=1''': the normalized peptide count for this peptide in charge state 1. | ||
- | **#'''log<sub>10</sub>(ω/ω<sub>0</sub>) z=2 | + | **#'''log<sub>10</sub>(ω/ω<sub>0</sub>) z=2''': the normalized peptide count for this peptide in charge state 2. |
- | **#'''ω | + | **#'''log<sub>10</sub>(ω/ω<sub>0</sub>) z=3''': the normalized peptide count for this peptide in charge state 3. |
- | + | ||
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. | 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. |
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.
Contents |
The default values for some of the search parameters are as follows:
A search can be performed with any combination of the following parameters:
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, any two masses between different results that differ by less than 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.
The Pattern parameter can be used to filter out results that do not match a given pattern. For help with the pattern syntax, a short tutorial can be seen at: Regular Expressions Quick Start.
The data returned by the search returns in the following order:
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.
The links below demonstrate the different search and display parameters (changeable parameters show in bold):