Abacus

Aggregate data from multiple experiments and adjusts label-free quantification to accurately account for peptides shared across multiple proteins

Usage

philosopher abacus [flags] [folders]

Flags

--comb

A pre formed combined protXML file. See below how to create one.

--labels

Indicates whether the data sets include TMT labels.

--pepProb

Minimum peptide probability (default 0.5).

--picked

Apply the picked FDR algorithm before the protein scoring.

--prtProb

Minimum protein probability (default 0.9).

--razor

Use razor peptides for protein FDR scoring.

--tag

Decoy tag (default "rev_").

--uniqueonly

Report TMT quantification based on only unique peptides.

Example

Aggregating data from 3 different experiments, in 3 different workspaces

philosopher abacus control/ treatment_1/ treatment_2/

Aggregating data from 3 different experiments, in 3 different workspaces and using a pre existing protXML combined file.

philosopher abacus --comb combined.potxml control/ treatment_1/ treatment_2/

FAQ

What exactly do I need to do before running Abacus ?

You need to work on each individual experiment workspace before running Abacus. Each folder containing individual experimental data must be converted to a Workspace and must have its data analyzed by the filter command.

I don't have a combined protXML file, how do I get one?

You need to execute ProteinProphet using all pepXML files from each individual folder you are analyzing.

Where should I execute the abacus command ?

The command should be execute one level above the experimental data

This seems to be a lot of work, isn't there any workaround ?

Yes, take a look at the Pipeline command.