userguide:peptidesandproteingrouping
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userguide:peptidesandproteingrouping [2010/04/14 10:56] 132.168.73.247 |
userguide:peptidesandproteingrouping [2012/03/29 09:02] (current) 132.168.72.131 |
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| ===== Algorithm ===== | ===== Algorithm ===== | ||
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| + | **Since hEIDI 1.11.0**, a new peptide/protein grouping algorithm has been implemented. This is part of a global idea which is to improve global performance in hEIDI.\\ | ||
| + | Indeed, datasets become bigger and bigger (ex. VELOS), and loading all data in memory in one hEIDI session is no more possible (as we did before hEIDI 1.11.0). \\ | ||
| + | The purpose is now to load the minimum information in hEIDI session, and to have algorithms that save results directly to MSIdb. \\ | ||
| + | We have started to optimize the peptide/Protein grouping algorithm as it requires to load a complex object tree and so is very memory consuming. Other algorithms will be optimized progressively in further hEIDI versions.\\ | ||
| + | |||
| + | **What are the changes for the user:** | ||
| + | * Paradoxically, the grouping is little bit slower compared to previous hEIDI versions. But, initial loading and save operation will be faster | ||
| + | * The MSIdb must be saved before launching grouping | ||
| + | * The peptide/protein grouping result is automatically saved to MSIdb | ||
| Protein grouping mechanism is detailled beneath the following image.\\ | Protein grouping mechanism is detailled beneath the following image.\\ | ||
| {{: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 | ||
| - | {{ :peptidegrouping.png|}} A new peptide is construct as follow : | + | {{ :peptidegrouping.png|}} A new peptide is construct as follow (since heidi 1.13.0) : |
| - | * ''charge, sequence, ptm, missed cleavage and calculated mass'' are copied from the first child peptide found | + | * ''peptide reference (sequence, ptm), missed cleavage and calculated mass'' are copied from the first child peptide found : |
| - | * ''experimental mass and retention time'' are set to childs average | + | * ''experimental mass, charge, delta mass, score, retention time and fragmentation count'' are copied from the best child : |
| - | * ''score'' is set to the max of child scores | + | |
| * ''child list'' is set as peptides with same sequence, same mass are found | * ''child list'' is set as peptides with same sequence, same mass are found | ||
| * 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. | ||
| Line 27: | Line 37: | ||
| - 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.1271235370.txt.gz · Last modified: 2010/04/14 10:56 by 132.168.73.247
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