prolineconcepts:lcmsquantitationadvancedconfig
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
prolineconcepts:lcmsquantitationadvancedconfig [2015/02/05 19:16] 193.48.0.3 |
prolineconcepts:lcmsquantitationadvancedconfig [2015/02/06 11:36] (current) 193.48.0.3 |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| ====== Post-processing of LC-MS quantitative results ====== | ====== Post-processing of LC-MS quantitative results ====== | ||
| - | This procedure is used to compute ratios of peptide and protein abundances and then to perform a statistical analysis. The significance of ratios varations is then computed at protein and protein levels using two statistical tests (T-Test and Z-Test). | + | This procedure is used to compute ratios of peptide and protein abundances. |
| Several filters can also be set to increase the quality of quantitative results. | Several filters can also be set to increase the quality of quantitative results. | ||
| Line 14: | Line 14: | ||
| * **Discard oxidized peptides**: if checked, peptides containing the Oxidation(M) modification will be discarded from the statistical analysis. It has to be noted that non-modified peptides whose sequence is the same than an observed oxidized peptide are also discarded if this option is enabled. | * **Discard oxidized peptides**: if checked, peptides containing the Oxidation(M) modification will be discarded from the statistical analysis. It has to be noted that non-modified peptides whose sequence is the same than an observed oxidized peptide are also discarded if this option is enabled. | ||
| - | === Peptide and protein statistical parameters === | + | === Peptide and protein common parameters === |
| - | * Normalization: | + | * Normalization: the normalization factors are computed as the median of the ratios distrubutions between each run and a run of reference. A similar procedure is used for the [[prolineconcepts:lcmslabelfreequantitationworkflow#median_of_ratios|normalization of LC-MS features]]. |
| - | + | ||
| - | par run en prenant une référence (1er run); sur la médiane de la distribution des ratios calculés entre chaque run et la référence | + | |
| - | + | ||
| - | * Statistical tests alpha: the p-value threshold used for the two statistical tests | + | |
| - | + | ||
| - | * T-Test: a Welch's modified T-Test (allows for unequal variance) used to assess the significance of the abundance mean difference between compared sample groups. | + | |
| - | + | ||
| - | * Z-Test: Z-scores are computed through a standardization procedure of observed log ratios => (log ratio - median_ratio)/log_ratios_standard_deviation. Z-scores (or standard scores) corresponds a number of standard deviations in the gaussian standard distribution. They can thus be easilly converted into p-values. | + | |
| === Aggregation of peptides in proteins === | === Aggregation of peptides in proteins === | ||
prolineconcepts/lcmsquantitationadvancedconfig.1423160185.txt.gz · Last modified: 2015/02/05 19:16 by 193.48.0.3
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
