prolineconcepts:lcmsquantitationadvancedconfig
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prolineconcepts:lcmsquantitationadvancedconfig [2015/02/05 19:20] 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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| * **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: 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]]. | * 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]]. | ||
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| - | * Statistical tests alpha: the p-value threshold used for the two statistical tests | ||
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| - | * 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. | ||
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| - | * 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.1423160402.txt.gz · Last modified: 2015/02/05 19:20 by 193.48.0.3
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