userguide:peptidesandproteingrouping
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userguide:peptidesandproteingrouping [2011/07/22 15:50] 132.168.73.124 |
userguide:peptidesandproteingrouping [2012/03/29 09:02] (current) 132.168.72.131 |
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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.\\ | **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 more and more 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). \\ | + | 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. \\ | 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.\\ | 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.\\ | ||
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| 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. | ||
userguide/peptidesandproteingrouping.1311342602.txt.gz · Last modified: 2011/07/22 15:50 by 132.168.73.124
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