userguide:retentiontimealignment
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userguide:retentiontimealignment [2010/08/02 11:00] 132.168.74.230 |
userguide:retentiontimealignment [2010/08/02 16:27] 132.168.74.230 |
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| ====== Retention Time Alignment ====== | ====== Retention Time Alignment ====== | ||
| - | Here are the major steps followed by the Retention Time algorithm: | ||
| - | Collect species from the reference User context and predict their retention time using an external utility | ||
| - | Collect species to align within identifications that are gathered under the reference User context | ||
| - | Constitute pair groups between collected reference species & species to align: a pair group is created from species having same sequence & calculated mass | ||
| - | In more details... | + | ===== Major steps followed by the Retention Time Alignment algorithm ===== |
| - | - Species Retention Time of the reference UserContext are predicted with **NETPrediction v2.2.3378** utility using Kangas method (click [[http://omics.pnl.gov/software/NETPredictionUtility.php|here]] for more details). NETPrediction utility only uses species **sequences** to predict a Normalized Elution Time (NET) value. First, a list of '//reference//' species is built with the below criteria, then the corresponding sequences are exported in order to be used by the NETPrediction utility: | + | {{ :userguide:rtalignmentconcept2.png|}} |
| - | * The reference species list doesn't contain any species with PTMs | + | - Collect species from the reference User context and predict their retention time using an external utility and store them in reference species properties |
| - | * If several species exist with redundant sequences, the best score species is retained | + | - For each identification gathered under the reference User context do: |
| - | - All the final child species, i.e. species in identifications, are collected. | + | - Collect species to align from the identification |
| - | + | - Constitute several pair groups between collected reference species & species to align. A pair group contains 2 groups of species having same sequence & calculated mass (group1 has species from reference User context and group2 has species to align from identifications). | |
| + | - Compute one (or several) representative value(s) for group1 & group2 for each pair group | ||
| + | - Compute linear regression between representative values | ||
| + | - Store linear regression coefficients & reference context name in identification properties | ||
| - | {{RtAlignmentConcept1.PNG}} | + | ===== In more details... ===== |
| - | {{:userguide:specif_alignement_tr_2.png|}} | + | {{ RtAlignmentConcept1.PNG}} |
| + | - Species Retention Time of the reference UserContext are predicted with **NETPrediction v2.2.3378** utility using Kangas method (click [[http://omics.pnl.gov/software/NETPredictionUtility.php|here]] for more details). NETPrediction utility only uses species **sequences** to predict a Normalized Elution Time (NET) value. | ||
| + | - First, a list of '//reference//' species is built | ||
| + | * The reference species list doesn't contain any species with PTMs | ||
| + | * If several species exist with redundant sequences, the best score species is retained | ||
| + | - Then, the corresponding sequences are exported in order to be used by the NETPrediction utility | ||
| + | - The predicted NET are converted to retention time using user-defined parameters (duration & delay). | ||
| + | - The user can decide to exclude predicted values too far from the others: | ||
| + | * The average absolute deviation (between RT & predicted RT) is computed and all predicted RT far from this average value about a given user-defined threshold are excluded. | ||
| + | - The predicted RT values are then stored as properties in the reference species. | ||
| + | - For each identification existing under the reference User context (not necessary directly under the reference user context): | ||
| + | - All the final child species to align are collected | ||
| + | - Several pair groups are created using reference species & species to align. A pair group contains 2 groups of species having same sequence & calculated mass (group1 has species from reference User context and group2 has species to align from identifications). | ||
| + | - For each group, according the statistical method choosen by the user, one or several representative RT value(s) is(are) calculated. | ||
| + | * Each 'Group1' always contains one species because [[userguide:proteingroups|species/protein grouping]] has been executed on the reference context and suppressed sequence/calculated mass redundancy. | ||
| + | * 'Group2' may contain one or more species. One or several representative value(s) is(are) calculated from one of following statistical methods: | ||
| + | * Average {{ :userguide:rtalignmentconcept3.png|}} | ||
| + | * Median | ||
| + | * Cross-product | ||
| + | * Combined | ||
| + | * Best score | ||
| + | - Compute linear regression between pair groups | ||
| + | - Store linear regression coefficients (slope/intercept) + reference context name in the identification properties | ||
userguide/retentiontimealignment.txt · Last modified: 2010/08/02 16:27 by 132.168.74.230
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