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maxquant:table:proteingrouptable
Protein groups
For a description of other output tables, see the directory.
The Protein Groups table contains information on the identified proteins in the processed raw-files. Each single row contains the group of proteins that could be reconstructed from a set of peptides.
| Name | Description |
|---|---|
| Protein IDs | Identifier(s) of protein(s) contained in the protein group. They are sorted by number of identified peptides in descending order. |
| Majority protein IDs | These are the IDs of those proteins that have at least half of the peptides that the leading protein has. |
| Peptide counts (all) | Number of peptides associated with each protein in protein group, occuring in the order as the protein IDs occur in the 'Protein IDs' column. Here distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide. |
| Peptide counts (razor+unique) | Number of peptides associated with each protein in protein group, occuring in the order as the protein IDs occur in the 'Protein IDs' column. Here distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide. |
| Peptide counts (unique) | Number of peptides associated with each protein in protein group, occuring in the order as the protein IDs occur in the 'Protein IDs' column. Here distinct peptide sequences are counted. Modified forms or different charges are counted as one peptide. |
| Protein names | Name(s) of protein(s) contained within the group. |
| Gene names | Name(s) of the gene(s) associated to the protein(s) contained within the group. |
| Mutated peptide count | |
| Mutation names | |
| “Mutated peptide count ” + exp | |
| “Mutation names ” + exp | |
| Fasta headers | Fasta headers(s) of protein(s) contained within the group. |
| Number of proteins | Number of proteins contained within the group. This corresponds to the number of entries in the colum 'Protein IDs'. |
| Peptides | The total number of peptide sequences associated with the protein group (i.e. for all the proteins in the group). |
| Razor + unique peptides | The total number of razor + unique peptides associated with the protein group (i.e. these peptides are shared with another protein group). |
| Unique peptides | The total number of unique peptides associated with the protein group (i.e. these peptides are not shared with another protein group). |
| “Peptides ” + exp | “Number of peptides (distinct peptide sequences) in experiment ” + exp |
| “Razor + unique peptides ” + exp | “Number of razor + unique peptides (distinct peptide sequences) in experiment ” + exp |
| “Unique peptides ” + exp | “Number of unique peptides (distinct peptide sequences) in experiment ” + exp |
| Sequence coverage [%] | Percentage of the sequence that is covered by the identified peptides of the best protein sequence contained in the group. |
| Unique + razor sequence coverage [%] | Percentage of the sequence that is covered by the identified unique and razor peptides of the best protein sequence contained in the group. |
| Unique sequence coverage [%] | Percentage of the sequence that is covered by the identified unique peptides of the best protein sequence contained in the group. |
| Mol. weight [kDa] | Molecular weight of the leading protein sequence contained in the protein group. |
| Sequence length | The length of the leading protein sequence contained in the group. |
| Sequence lengths | The length of all sequences of the proteins contained in the group. |
| Fraction average | |
| “Fraction ” + t | |
| Q-value | This is the ratio of reverse to forward protein groups. |
| Score | Protein score which is derived from peptide posterior error probabilities. |
| “Identification type ” + exp | Indicates whether this experiment was identified by MS/MS or only by matching between runs. |
| “Sequence coverage ” + exp + “ [%]” | Percentage of the sequence that is covered by the identified peptides in this sample of the longest protein sequence contained within the group. |
| Only identified by site | When marked with '+', this particular protein group was identified only by a modification site. |
| Reverse | When marked with '+', this particular protein group contains no protein, made up of at least 50% of the peptides of the leading protein, with a peptide derived from the reversed part of the decoy database. These should be removed for further data analysis. The 50% rule is in place to prevent spurious protein hits to erroneously flag the protein group as reverse. |
| Potential contaminant | When marked with '+', this particular protein group was found to be a commonly occurring contaminant. These should be removed for further data analysis. |
| id | A unique (consecutive) identifier for each row in the proteinGroups table, which is used to cross-link the information in this file with the information stored in the other files. |
| Peptide IDs | Identifier(s) of the associated peptide sequence(s) summary, which can be found in the file 'peptides.txt'. |
| Peptide is razor | Indicates for each peptide ID if it is a razor or group unique peptide (true) or a non unique non razor peptide (false). |
| Mod. peptide IDs | |
| Evidence IDs | |
| MS/MS IDs | |
| Best MS/MS | The identifier of the best (in terms of quality) MS/MS scans identifying the peptides of this protein, referenced against the msms table. |
| t + “ site IDs” | Identifier(s) for site(s) associated with the protein group, which show(s) evidence of the modification, referenced against the appropriate modification site file. |
| t + “ site positions” | Positions of the sites in the leading protein of this group. |
| “LFQLabel-free quantification intensity L ” + exp | |
| “LFQ intensity M ” + exp | |
| “LFQ intensity H ” + exp | |
| “LFQ intensity L ” + exp | |
| “LFQ intensity H ” + exp | |
| “LFQ intensity ” + exp | |
| “iBAQIntensity Based Absolute Quantification ” + exp | |
| “iBAQ L ” + exp | |
| “iBAQ M ” + exp | |
| “iBAQ H ” + exp | |
| iBAQ | |
| iBAQ L | |
| iBAQ M | |
| iBAQ H | |
| “iBAQ ” + exp | |
| “iBAQ L ” + exp | |
| “iBAQ H ” + exp | |
| iBAQ | |
| iBAQ L | |
| iBAQ H | |
| “iBAQ ” + exp | |
| iBAQ | |
| AVALON | |
| MS/MS Count | |
| “MS/MS Count ” + exp | |
| “Intensity ” + exp | Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. |
| “Intensity L ” + exp | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the light label partner. |
| “Intensity M ” + exp | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the medium label partner. |
| “Intensity H ” + exp | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the heavy label partner. |
| Intensity | Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. |
| Intensity L | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the light label partner. |
| Intensity M | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the medium label partner. |
| Intensity H | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the heavy label partner. |
| “Intensity ” + exp | Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. |
| “Intensity L ” + exp | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the light label partner. |
| “Intensity H ” + exp | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the heavy label partner. |
| Intensity | Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. |
| Intensity L | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the light label partner. |
| Intensity H | Summed up eXtracted Ion Current (XIC) of the isotopic cluster linked to the heavy label partner. |
| “Intensity ” + exp | Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. |
| Intensity | Summed up eXtracted Ion Current (XIC) of all isotopic clusters associated with the identified AA sequence. In case of a labeled experiment this is the total intensity of all the isotopic patterns in the label cluster. |
| “Ratio M/L ” + exp | The ratio between two medium and light label partners. |
| “Ratio M/L normalized ” + exp | Normalized ratio between two heavy and light label partners. The median of the total ratio population was shifted to 1. |
| “Ratio M/L variability [%] ” + exp | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| “Ratio M/L count ” + exp | Number of redundant peptides (MS1 features) used for quantitation. |
| “Ratio M/L iso-count ” + exp | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| “Ratio M/L type ” + exp | |
| “Ratio H/L ” + exp | The ratio between two heavy and light label partners. |
| “Ratio H/L normalized ” + exp | Normalized ratio between two medium and light label partners. The median of the total ratio population was shifted to 1. |
| “Ratio H/L variability [%] ” + exp | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| “Ratio H/L count ” + exp | Number of redundant peptides (MS1 features) used for quantitation. |
| “Ratio H/L iso-count ” + exp | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| “Ratio H/L type ” + exp | |
| “Ratio H/M ” + exp | The ratio between two heavy and medium label partners. |
| “Ratio H/M normalized ” + exp | Normalized ratio between two heavy and medium label partners. The median of the total ratio population was shifted to 1. |
| “Ratio H/M variability [%] ” + exp | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| “Ratio H/M count ” + exp | Number of redundant peptides (MS1 features) used for quantitation. |
| “Ratio H/M iso-count ” + exp | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| “Ratio H/M type ” + exp | |
| Ratio M/L | The ratio between two medium and light label partners. |
| Ratio M/L normalized | Normalized ratio between two heavy and light label partners. The median of the total ratio population was shifted to 1. |
| Ratio M/L variability [%] | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| Ratio M/L count | Number of redundant peptides (MS1 features) used for quantitation. |
| Ratio M/L iso-count | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| Ratio M/L type | |
| Ratio H/L | The ratio between two heavy and light label partners. |
| Ratio H/L normalized | Normalized ratio between two medium and light label partners. The median of the total ratio population was shifted to 1. |
| Ratio H/L variability [%] | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| Ratio H/L count | Number of redundant peptides (MS1 features) used for quantitation. |
| Ratio H/L iso-count | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| Ratio H/L type | |
| Ratio H/M | The ratio between two heavy and medium label partners. |
| Ratio H/M normalized | Normalized ratio between two heavy and medium label partners. The median of the total ratio population was shifted to 1. |
| Ratio H/M variability [%] | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| Ratio H/M count | Number of redundant peptides (MS1 features) used for quantitation. |
| Ratio H/M iso-count | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| Ratio H/M type | |
| “Ratio H/L ” + exp | The ratio between two heavy and light label partners. |
| “Ratio H/L normalized ” + exp | Normalized ratio between two medium and light label partners. The median of the total ratio population was shifted to 1. |
| “Ratio H/L variability [%] ” + exp | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| “Ratio H/L count ” + exp | Number of redundant peptides (MS1 features) used for quantitation. |
| “Ratio H/L iso-count ” + exp | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| “Ratio H/L type ” + exp | |
| Ratio H/L | The ratio between two heavy and light label partners. |
| Ratio H/L normalized | Normalized ratio between two medium and light label partners. The median of the total ratio population was shifted to 1. |
| Ratio H/L variability [%] | Coefficient of variability over all redundant quantifiable peptides. It is calculated as the standard deviation of the naturally logarithmized ratios times 100. |
| Ratio H/L count | Number of redundant peptides (MS1 features) used for quantitation. |
| Ratio H/L iso-count | Number of redundant peptides (MS1 features) used for quantitation that are quantified with the re-quantify method. |
| Ratio H/L type | |
| “Reporter intensity ” + i | |
| “Reporter intensity not corrected ” + i | |
| “Reporter intensity count ” + i | |
| “Reporter intensity ” + i + “ ” + exp | |
| “Reporter intensity not corrected ” + i + “ ” + exp | |
| “Reporter intensity count ” + i + “ ” + exp |
maxquant/table/proteingrouptable.txt · Last modified: 2015/11/23 14:37 (external edit)
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