Perform Volcano plot analysis on selected experimental conditions followed by MS search on significant features

Group1Experimental factorGroup2
Diet:- | Study Phenotype:Pooled | Treatment:- | Liver Lobe:- (18)
Diet:HCHF | Study Phenotype:15 wk Differential Diet | Treatment:None | Liver Lobe:Left (8)
Diet:HCHF | Study Phenotype:15 wk Differential Diet | Treatment:None | Liver Lobe:Median (8)
Diet:HCHF | Study Phenotype:15 wk Differential Diet | Treatment:None | Liver Lobe:Right (8)
Diet:HCHF | Study Phenotype:24 hr Treatment | Treatment:DOX-treated | Liver Lobe:Left (3)
Diet:HCHF | Study Phenotype:24 hr Treatment | Treatment:DOX-treated | Liver Lobe:Median (3)
Diet:HCHF | Study Phenotype:24 hr Treatment | Treatment:DOX-treated | Liver Lobe:Right (3)
Diet:HCHF | Study Phenotype:24 hr Treatment | Treatment:Saline-control | Liver Lobe:Left (3)
Diet:HCHF | Study Phenotype:24 hr Treatment | Treatment:Saline-control | Liver Lobe:Median (3)
Diet:HCHF | Study Phenotype:24 hr Treatment | Treatment:Saline-control | Liver Lobe:Right (3)
Diet:HCHF | Study Phenotype:Tumor Growth-5 wk | Treatment:None | Liver Lobe:Left (2)
Diet:HCHF | Study Phenotype:Tumor Growth-5 wk | Treatment:None | Liver Lobe:Median (2)
Diet:HCHF | Study Phenotype:Tumor Growth-5 wk | Treatment:None | Liver Lobe:Right (2)
Diet:HCHF | Study Phenotype:Tumor Growth-5.5 wk | Treatment:None | Liver Lobe:Left (10)
Diet:HCHF | Study Phenotype:Tumor Growth-5.5 wk | Treatment:None | Liver Lobe:Median (9)
Diet:HCHF | Study Phenotype:Tumor Growth-5.5 wk | Treatment:None | Liver Lobe:Right (10)
Diet:HP | Study Phenotype:15 wk Differential Diet | Treatment:None | Liver Lobe:Left (8)
Diet:HP | Study Phenotype:15 wk Differential Diet | Treatment:None | Liver Lobe:Median (8)
Diet:HP | Study Phenotype:15 wk Differential Diet | Treatment:None | Liver Lobe:Right (8)
Diet:HP | Study Phenotype:24 hr Treatment | Treatment:DOX-treated | Liver Lobe:Left (3)
Diet:HP | Study Phenotype:24 hr Treatment | Treatment:DOX-treated | Liver Lobe:Median (3)
Diet:HP | Study Phenotype:24 hr Treatment | Treatment:DOX-treated | Liver Lobe:Right (3)
Diet:HP | Study Phenotype:24 hr Treatment | Treatment:Saline-control | Liver Lobe:Left (3)
Diet:HP | Study Phenotype:24 hr Treatment | Treatment:Saline-control | Liver Lobe:Median (3)
Diet:HP | Study Phenotype:24 hr Treatment | Treatment:Saline-control | Liver Lobe:Right (3)
Diet:HP | Study Phenotype:Baseline | Treatment:None | Liver Lobe:Left (8)
Diet:HP | Study Phenotype:Baseline | Treatment:None | Liver Lobe:Median (8)
Diet:HP | Study Phenotype:Baseline | Treatment:None | Liver Lobe:Right (8)
Diet:HP | Study Phenotype:Tumor Growth-5 wk | Treatment:None | Liver Lobe:Left (2)
Diet:HP | Study Phenotype:Tumor Growth-5 wk | Treatment:None | Liver Lobe:Median (2)
Diet:HP | Study Phenotype:Tumor Growth-5 wk | Treatment:None | Liver Lobe:Right (2)
Diet:HP | Study Phenotype:Tumor Growth-5.5 wk | Treatment:None | Liver Lobe:Left (8)
Diet:HP | Study Phenotype:Tumor Growth-5.5 wk | Treatment:None | Liver Lobe:Median (8)
Diet:HP | Study Phenotype:Tumor Growth-5.5 wk | Treatment:None | Liver Lobe:Right (10)

Filtering Parameters
Select threshold % for selection below:
Option 1: No filtering
Option 2: Filter by Sum (Analytes whose sum for all samples falls below the threshold % will be excluded)
Option 3: Filter by Mean (Analytes whose mean for all samples falls below the threshold % will be excluded)
Option 4: Filter by Median (Analytes whose median for all samples falls below the threshold % will be excluded)
Option 5: Filter by Sample threshold       must exceed the above threshold per analyte
In order for an analyte to be retained, the % of samples in one/both groups which are non-zero must exceed the threshold.
Option 6: Remove all analytes containing null values
Sample Normalization Parameters
Normalize samples by:
Volcano Plot Parameters
P-value cutoff: Fold-change cutoff:
MS Search Parameters
Search Refmet database
MS Ion polarity:POSITIVE MS search m/z tolerance:
Ion adducts(choose at least one)
Positive mode:
 [M+H]+ [M+H-H2O]+ [M+Na]+ [M+NH4]+ [M+K]+ [M+2H]2+ [M+2Na]2+ [M+2Na-H]+
[M+H-EtnP]+ [M+H-SerP]+
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