What's this?

This is a sub project of altorf, analyzing altorf from proteome perspective. By executing peptide identification with various sequence database using MS-GF+, we can find those peptides which is missing from annotation, but actually translated. PNNL library was used as MS/MS data inputs.

Workflow

Follow this flow from top to bottom. For further information, please refer to README on each sub directories.

0. createcatalog

   • Organizes scattered information about the 112 species in PNNL library.

1. pickdatasets

   • Picks datasets to analyze, considering MS/MS type and the number of identified peptides.

2. downloadpnnl

   • Downloads picked .mzML, .mzid & .fasta files from PNNL library ftp.

3. extractparam

   • Extracts information from each .mzids on the MS-GF+ configuration for peptide identification.

4. createsequence

   • Creates various sequences database for peptide identification.

5. exec

   • Executes peptide identification using MS-GF+.

6. processresult

Prerequisites

• MS-GF+
  • performs peptide identification
  • requires >=JRE 1.6 and Main maemory >=2GB
• Anaconda (ver 3.X)
• BioPython