MANTI.pl / muda.pl Files

-> muda.pl - MQ unified data assembler . pl README

muda.pl is an evaluation script (written in Perl) without great dependencies.
It congregates information from 4 different MaxQuant output files into a master 
file suitable explicitly for protein neo-termini analyses. Maybe also useful for 
normal proteomics purposes but this script is heavily optimized for protein
neo-termini identification and validation. The central anchor for the data
congregation is the modificationSpecificPeptides.txt file - additional data is 
inferred from different other source files from the MaxQuant txt folder but the 
starting point for the data assembly is solely the 
modificationSpecificPeptides.txt file.

For a more thorough explanation of script parameters and evaluation strategy, 
please consult the handbook .PDF.

COPYRIGHT/AUTHOR: 2017-2019, Fatih Demir <f.demir@fz-juelich.de>

LICENSE: Perl Artistic License 2.0 as supplemented in the "LICENSE" file

REQUIREMENTS:

- MaxQuant output "txt" Folder/or at least a folder containing the following 
MaxQuant txt files:
	- modificationSpecificPeptides.txt
	- peptides.txt
	- proteinGroups.txt
	- summary.txt

- Perl interpreter (users of Windows need to use e.g. the PowerShell and call 
muda.pl as "perl muda.pl")


OPTIONAL:

- Internet access (for UniProt data retrieval in case of extended annotation 
retrieval).


EXAMPLE USES:

NO 1:

./muda.pl -a -s -b -z -i MQ_DIR/ -o MUDA_OUTPUT_DIR -m MUDA.txt
- OR -
./muda.pl -y -i MQ_DIR/ -o MUDA_OUTPUT_DIR -m MUDA.txt

Ready in the MQ txt folder from MQ_DIR and puts evaluated masterfile into 
MUDA.txt and the remaining analysis files into the newly created directory
MUDA_OUTPUT_DIR. Additionally annotates (-a) files via UniProt and displays 
only cleavage sites in the vicinity of max. 5 aas from UniProt features (-b).
Also use a shortened localization mapping without sub-compartments (-s) and AA
maps build upon the identified peptides are sorted by amino acid stability (-z),
according to N-end rule.

NO 2:

./muda.pl -i MQ_DIR

Lazy people version without internet access - just assemble the data from 
MQ_DIR into a newly created folder MUDA_PL_DIR_TIMESTAMP and the new master file
muda_pl_TIMESTAMP.txt.

NO 3:

./muda.pl -a -e -i MQ_DIR -o EXPERIMENT_DIR -m Super.txt --join-top 
Full_Table.txt --lowest-int 1000

Take MQ_DIR, annotate via UniProt, set lowest intensity threshold for own Int 
ratio buildup to 1000 intensities (regardless of minimum in measurements -
normally, this is defined automatically).
Integrate TopFinder Full_Table.txt for localization & cleavage information into 
the new master file Super.txt. Also supply expanded sub-compartment localization
tagging from UniProt.

NO 4:

./muda.pl -y -i MQ_DIR -o EXPERIMENT_DIR -m Super.txt -g database_peptides.txt

Annotate and fill information into Super.txt; also implement the newly analyzed 
peptides from Super.txt into a new database-like big "master file"
database_peptides.txt to join all analyzed together into one file complementing
information from many experiments.