userguide:peptidesandproteingrouping
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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userguide:peptidesandproteingrouping [2010/04/14 10:56] 132.168.73.247 |
userguide:peptidesandproteingrouping [2010/07/28 15:12] 132.168.74.230 |
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| {{:proteingroupingmechanism.png| Protein grouping mechanism}} | {{:proteingroupingmechanism.png| Protein grouping mechanism}} | ||
| ==== Step 1 - Peptide grouping ==== | ==== Step 1 - Peptide grouping ==== | ||
| + | === grouping === | ||
| {{:GroupingStep1.png |}} Peptides from different child context or identifications - attached directly or indirectly to a context - are grouped.\\ | {{:GroupingStep1.png |}} Peptides from different child context or identifications - attached directly or indirectly to a context - are grouped.\\ | ||
| - | Peptides must have same sequence and same experimental mass to be grouped. \\ | + | Peptides must have same sequence and same calculated mass to be grouped. \\ |
| Peptide grouping results in **new** peptides attached to the parent context and having child peptides | Peptide grouping results in **new** peptides attached to the parent context and having child peptides | ||
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| * to define the ''matches list'' associated to new peptide, matches from all child peptides are grouped using matched protein. Created match ''score'' is set to the max of all child matches scores and ''start and end'' value are equal to child matches start and end. | * to define the ''matches list'' associated to new peptide, matches from all child peptides are grouped using matched protein. Created match ''score'' is set to the max of all child matches scores and ''start and end'' value are equal to child matches start and end. | ||
| + | === filtering === | ||
| Different filters could be applied during grouping. | Different filters could be applied during grouping. | ||
| - First protein filter is applied while creating the list of proteins to which match each peptide. (filter reverse protein for instance). This is done before ''new matches'' are created. | - First protein filter is applied while creating the list of proteins to which match each peptide. (filter reverse protein for instance). This is done before ''new matches'' are created. | ||
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| - The last filter allow user to filter new grouped peptides. | - The last filter allow user to filter new grouped peptides. | ||
| - | The filtered protein or species are not taken into account in the final grouping result, they are removed from result (unlike during protein filter (FIXME add link)). An other difference with ''protein filter'' operation is that filtering is done on each proteins. | + | The filtered protein or species are not taken into account in the final grouping result, they are removed from result (unlike during [[userguide:proteinfiltering|protein filter]] ). An other difference with ''protein filter'' operation is that filtering is done on each proteins. |
userguide/peptidesandproteingrouping.txt · Last modified: 2012/03/29 09:02 by 132.168.72.131
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