Abacus

Aggregate data from multiple experiments and adjust label-free quantification for peptides shared across multiple proteins with Abacus

Usage

philosopher abacus [flags] [folders]

Flags

--peptide

Global level peptide report (needs a combined.pep.xml file).

--protein

Global level protien report (needs a combined.prot.xml file).

--labels

Indicates whether the data sets include TMT labels or not.

--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.

--reprint

Create abacus reports using the Reprint format

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 --protein 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 pepXML file, how do I get one?

You need to execute iProphet using all interact.pep.xml files from each individual folder you are analyzing.

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.