Join Quant Peptide-Ions With Proteins

Disclaimer this tool needs the results from ProteinInference and PSMBasedQuantification.

Results from PSMBasedQuantification contain detailed information about the quantification of every peptide, but only basic informations about the protein they originated from. This information is obtained during the ProteinInference. This tool takes the results from both tools and combines the qauntification information of each peptide with the more accurate information about the corresponding protein including its q-value.

Executing the Tool

Disclaimer this tool needs the results from ProteinInference and PSMBasedQuantification.

To combine all quantified peptides with their infered protein simply call:

proteomiqon-joinquantpepionswithproteins -i "path/to/your/run/quant" -ii "path/to/your/run/prot" -o "path/to/your/outDirectory"

It is also possible to call the tool on a list of qaunt and prot files:

proteomiqon-joinquantpepionswithproteins -i "path/to/your/run1.quant" "path/to/your/run2.quant" "path/to/your/run3.quant" -ii "path/to/your/run1.prot" "path/to/your/run2.prot" "path/to/your/run3.prot" -o "path/to/your/outDirectory"

A detailed description of the CLI arguments the tool expects can be obtained by calling the tool:

proteomiqon-joinquantpepionswithproteins --help