MANTI Files

-> MANTI.pl - Mastering Advanced N-Termini Interpretion . pl README

MANTI.pl is an evaluation script (written in Perl) without great dependencies.
It aggregates information from different MaxQuant DDA / DiaNN/MSFragger search
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 aggregating the data is the modificationSpecificPeptides.txt file for MaxQuant or
the diann-output.pr_matrix.tsv for DiaNN/MSFragger searches - additional data is 
inferred from other source files from the MaxQuant txt/DiaNN MSFragger search folder
but the  starting point for the data assembly is the modificationSpecificPeptides.txt 
or diann-output.pr_matrix.tsv file.

For a more thorough explanation of script parameters and evaluation strategy, 
please consult the handbook .PDF or the help parameter by calling MANTI on
the command line like the following:

perl MANTI.pl --help

Additionally, a GUI is available, called Yoğurtlu MANTI which is shipped together
with each MANTI release and can be run on the command line via:

perl Yogurtlu_MANTI.pl

If you are using Windows10 and do not have any Perl installation, you can use the

"Yogurtlu_MANTI.exe" file directly which should be a self-contained version of the
GUI interface together with MANTI (so you can run this .exe file within the MANTI
sources for running the MANTI analysis without the need for a local Perl installation).

COPYRIGHT/AUTHOR: 2017-2022, Fatih Demir <fatih.demir@biomed.au.dk>

LICENSE: Perl Artistic License 2.0 as supplemented in "docs/LICENSE.txt".

REQUIREMENTS:

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

- OR ALTERNATIVELY -

B) DiaNN/MSFragger DIA search results containing the following source files:
	- diann-output.pr_matrix.tsv
	- fragger_dia.params
	- ion.tsv
	- protein.tsv
	- psm.tsv

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


OPTIONAL:

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

- R (with ggplot2, ggcorrplot and some other useful packages installed) for
plotting of volcano plots and a plethora of different informative plots. To help
the installation of all the required R packages, simply make use of the R script
"MANTI_R_InstallPackages.R" supplied within the docs directory, it will install
automatically all missing libraries in R. Simply drop the file into your R window
or call it within R with the following command:

source("MANTI_R_InstallPackages.R")

EXAMPLE USES:

NO 1:

perl MANTI.pl -a -s -b -z --input-mq MQ_DIR/ -o MANTI_OUTPUT_DIR -m MANTI.txt
- OR -
perl MANTI.pl -y --input-mq MQ_DIR/ -o MANTI_OUTPUT_DIR -m MANTI.txt

Ready in the MQ txt folder from MQ_DIR and puts evaluated masterfile into 
MANTI.txt and the remaining analysis files into the newly created directory
MANTI_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:

perl MANTI.pl --input-mq MQ_DIR

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

NO 3:

perl MANTI.pl -a -e --input-mq MQ_DIR -o EXPERIMENT_DIR -m Super.txt --join-top 
Full_Table.txt --threshold 1000

Take MQ_DIR, annotate via UniProt, set lowest intensity threshold for own Int 
ratio buildup to 1000 intensities (regardless of minimum in the measurements -
normally, this is defined automatically as the lowest intensity - 1 by default).
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:

perl MANTI.pl -y --input-mq 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.

NO 5:

perl MANTI.pl -y --input-mq MQ_DIR -o SUPER_DIR -m Super.txt --terminator

Run MANTI in terminator mode to automatically run the supplied R scripts polvops.R
for limma-statistics and bufipretty.R to produce graphs in the correct order and
without any further user action.

NO 6:

perl MANTI.pl -y --input-diafragger DIAMSFRAGGER_DIR -o SUPER_DIR -m Super.txt

Run MANTI with the corresponding DiaNN/MSFragger search - will yield a similar
output file as for simplex MaxQuant searches.