prolineconcepts:lcmsquantitationadvancedconfig
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prolineconcepts:lcmsquantitationadvancedconfig [2015/02/05 19:15] 193.48.0.3 |
prolineconcepts:lcmsquantitationadvancedconfig [2015/02/06 11:36] (current) 193.48.0.3 |
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| ====== 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. | ||
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| === Peptide filters === | === Peptide filters === | ||
| - | * **Use only specific peptides**: if checked, peptides shared between different protein sets will be discarded from the statistical analysis. | + | * **Use only specific peptides**: if checked, peptides shared between different protein sets will be discarded from the statistical analysis. |
| - | * **Discard missed cleaved peptides**: if checked, peptides containing missed cleavages will be discarded from the statistical analysis. It has to be noted that perfect tryptic peptides whose sequence is included in an observed missed cleaved peptide are also discarded if this option is enabled. | + | * **Discard missed cleaved peptides**: if checked, peptides containing missed cleavages will be discarded from the statistical analysis. It has to be noted that perfect tryptic peptides whose sequence is included in an observed missed cleaved 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. | + | * **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 === |
| - | * Normalisation: | + | * 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.1423160129.txt.gz · Last modified: 2015/02/05 19:15 by 193.48.0.3
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