labelquant

Protein quantification based on isobaric labeling (TMT or iTRAQ).

Usage

philosopher labelquant [flags]

Flags

--annot

Annotation file with custom names for the TMT channels. See below how to format your annotation file.

--dir

Folder path containing the raw files.

--plex

Number of channels.

--level

MS level for the quantification (default 2)

--purity

Precursor ion purity threshold (default 0.5).

--tol

M/Z tolerance in PPM (default "10").

--uniqueonly

Report quantification based on only unique peptides.

--removelow

Ignore the lower % of PSMs based on their summed abundances. 0 Means no removal, entry value must be decimal.

Example

A 10-plex TMT analysis:

philosopher labelquant --plex 10 --dir mz/

FAQ

How to format my annotation file ?

The annotation file is a simple text (.txt) file named annotation.txt. Each line must contain only 2 words, the first one is the TMT label and the second one the custom name you want to use. Do not add headers to the file.

example

126 control1
127N control2
127C control3
128N treatment_1
128C treatment_1
129N treatment_2
129C treatment_2
130N treatment_3
130C treatment_3
131N pool_1