To specify which columns to display for protein results when viewing an MS2 run, use the guidance in this topic.
The currently displayed columns appear in the Selected Fields pane. You can edit the columns that appear in this list manually for finely tuned control over which columns are displayed in what order.
The following table describes some of the available protein columns. Not all columns are available for all data sets.
| Protein Column | Column Abbrev | Description |
|---|---|---|
| Protein | The name of the sequence from the protein database. | |
| SequenceMass | The mass of the sequence calculated by adding the masses of its amino acids. | |
| Peptides | PP Peps | The number of filtered peptides in the run that were matched to this sequence. |
| UniquePeptides | PP Unique | The number of unique filtered peptides in the run that were matched to this sequence. |
| AACoverage | The percent of the amino acid sequence covered by the matched, filtered peptides. | |
| BestName | A best name, either an accession number or descriptive word, for the identified protein. | |
| BestGeneName | The most useful gene name associated with the identified protein. | |
| Description | Short description of the protein’s nature and function. | |
| GroupNumber | Group | A group number assigned to the ProteinProphet group. |
| GroupProbability | Prob | ProteinProphet probability assigned to the protein group. |
| PctSpectrumIds | Spectrum Ids | Percentage of spectrum identifications belonging to this protein entry. As a semi-quantitative measure, larger numbers reflects higher abundance. |
| ErrorRate | The error rate associated with the ProteinProphet probability for the group. | |
| ProteinProbability | Prob | ProteinProphet probability assigned to the protein(s). |
| FirstProtein | ProteinProphet entries can be composed of one or more indistinguishable proteins and are reflected as a protein group. This column represents the protein identifier, from the protein sequence database, for the first protein in a protein group. | |
| FirstDescription | Protein description of the FirstProtein. | |
| FirstGeneName | Gene name, if available, associated with the FirstProtein. | |
| FirstBestName | The best protein name associated with the FirstProtein. This name may come from another protein database file. | |
| RatioMean | L2H Mean | The light-to-heavy protein ratio generated from the mean of the underlying peptide ratios. |
| RatioStandardDev | L2H StdDev | The standard deviation of the light-to-heavy protein ratio. |
| RatioNumberPeptides | Ratio Peps | The number of quantified peptides contributing to the protein ratio. |
| Heavy2LightRatioMean | H2L Mean | The heavy-to-light protein ratio generated from the mean of the underlying peptide ratios. |
| Heavy2LightRatioStandardDev | H2L StdDev | The heavy-to-light standard deviation of the protein ratio. |
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