(New page: The ''peptide'' table records the details for each peptide identification, which is in turn used to identify the proteins in a GPM result file. If a ...) |
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The ''peptide'' table records the details for each peptide identification, which is in turn used to identify the [[Technical Overview, protein table|proteins]] in a GPM result file. If a GPM [[Technical Overview, result table|result]] file had no successful protein identifications, there will be no entries in the ''peptide'' table associated with it through the [[Technical Overview, protein table|protein]] table. | The ''peptide'' table records the details for each peptide identification, which is in turn used to identify the [[Technical Overview, protein table|proteins]] in a GPM result file. If a GPM [[Technical Overview, result table|result]] file had no successful protein identifications, there will be no entries in the ''peptide'' table associated with it through the [[Technical Overview, protein table|protein]] table. | ||
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| + | The contents of this table are updated incrementally as part of the [[Technical Overview, GPMDB Updates|update]] procedure which executes daily. | ||
Columns: | Columns: | ||
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*'''proid''': the unique identifier for the protein with which this peptide identification is associated. | *'''proid''': the unique identifier for the protein with which this peptide identification is associated. | ||
*'''seq''': the residue sequence of the peptide. | *'''seq''': the residue sequence of the peptide. | ||
| - | *'''mh''': the mass | + | *'''mh''': the mass (in Daltons) of the peptide, as measured by the instrument which generated the original data file. |
| - | *'''expect''': the base-10 logarithm of the chance that the identification of this | + | *'''expect''': the base-10 logarithm of the chance that the identification of this peptide was an accidental random match. E.g., if the '''expect''' value is -4.0, the odds of this peptide identification being a random match are 1 in 10,000. |
*'''start''': the start location of this peptide's residue sequence in its associated protein residue sequence. | *'''start''': the start location of this peptide's residue sequence in its associated protein residue sequence. | ||
*'''end''': the end location of this peptide's residue sequence in its associated protein residue sequence. | *'''end''': the end location of this peptide's residue sequence in its associated protein residue sequence. | ||
*'''charge''': the charge of the ion as measured by the insturment which generated the original data file. | *'''charge''': the charge of the ion as measured by the insturment which generated the original data file. | ||
| - | *'''delta''': the difference between the mass | + | *'''delta''': the difference between the mass as measured by the instrument and the theoretically calculated mass given the peptide's residue sequence. |
*'''dida''': the 1-based sequence of this mass spectrum in the original data file. | *'''dida''': the 1-based sequence of this mass spectrum in the original data file. | ||
*'''didb''': the identifier for this particular mass spectrum. | *'''didb''': the identifier for this particular mass spectrum. | ||
*'''didc''': the 1-based sequence of specific measurement of this mass spectrum. | *'''didc''': the 1-based sequence of specific measurement of this mass spectrum. | ||
The peptide table records the details for each peptide identification, which is in turn used to identify the proteins in a GPM result file. If a GPM result file had no successful protein identifications, there will be no entries in the peptide table associated with it through the protein table.
The contents of this table are updated incrementally as part of the update procedure which executes daily.
Columns: