This is a command-line script to map tryptic peptides to Lys-C peptides. The program expects a FASTA-file and a "peptides.txt" file from MaxQuant as input, and will generate two tab delimited text files as output. The first results file, definable using the "-lysc" option, generates the LysC peptide sequences as well as start and end positions within given proteins. The second results file, definable using the "-ptm" option, is used as input for Perseus.
Mullari M, Lyon D, Jensen LJ, Nielsen ML, Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification. Journal of Proteome Research, 2017. DOI: 10.1021/acs.jproteome.7b00042 https://www.ncbi.nlm.nih.gov/pubmed/28648085
This script can be run on any operating system (Windows, Mac OSX, Linux) running Python. - Python 2.x - Python packages: numpy, pandas
type "-h" or "--help" for help.
e.g. type the following command in the terminal to see options.
python tryptic2LysC.py -h
python tryptic2LysC.py -fasta /Directory/FastaFileName.fasta -mq /Directory/MaxQuant_peptides.txt -lysc /Directory/Results_LYSC.txt -ptm /Directory/Results_PTM.txt
python tryptic2LysC.py -fasta C:\Directory\FastaFileName.fasta -mq C:\Directory\MaxQuant_peptides.txt -lysc C:\Directory\Results_LYSC.txt -ptm C:\Directory\Results_PTM.txt
feel free to contact david.lyon@cpr.ku.dk for help!