PINCIS Files

-> PINCIS.pl - PIcs N-/C-terminal Inferred Substrates perl script . pl README

PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small,
command line tool to designate and analyze PICS (Schilling et al., Nat.
Protocols, 2011) data to gain the prime and non-prime site specificity of
proteases. Thus, the script filters given peptide lists for library peptides
(generated by the digestion protease in the proteomics workflow rather then
the protease of interest) and prints out lists of inferred N- and C-terminal
cleavage window extensions which can be concurrently used to generate cleavage
specificity visuals, e.g. iceLogo (https://iomics.ugent.be/icelogoserver/create).

A helpful, explanatory information message is displayed when PINCIS.pl is called
with the "--help" argument ("perl PINCIS.pl --help").

COPYRIGHT/AUTHOR: 2016-2020, Fatih Demir <fatih.demir@biomed.au.dk>

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

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REQUIREMENTS:

- Peptide list as a text file

	A newline separated list of peptides, already filtered for protease activity.
	Standard filters would be to select only peptides which are at least 4-fold
	upregulated upon active protease addition or only detectable in the protease
	sample - the combined list of both conditions will give you the peptide list
	which is parsed by PINCIS argument --peptides.

- FASTA file

	You need to supply the FASTA file of the PICS library applied in the PICS
	assay - most likely this will be an E. coli library, thus the E.coli FASTA
	is supplied with PINCIS. But if you have a PICS assay on a different library
	like mouse cell lines etc., then you need to supply the corresponding FASTA
	database here with the --fasta argument of PINCIS.

- Knowledge of the digestion protease

	You have to set the digestion protease used in your proteomics experiment,
	e.g. trypsin with the --enzyme argument of PINCIS.
	Currently accepted proteases are:
	
		- Trypsin (cleaves after K/R)
		- GluC (D/E)
		- Legumain (D/N)
		- Chymotrypsin (F/Y/W/L)
	
	You can also just enter the first character of the protease while giving the
	--enzyme argument, e.g. "--enzyme T" instead of fully typing in Trypsin. If
	no enzyme is defined, PINCIS.pl assumes automatically that trypsin was used.

- Perl interpreter:

	Users of Windows need to use e.g. the PowerShell and call PINCIS.pl
	as "perl PINCIS.pl". There are many Perl distributions freely available
	for a multitude of operating systems, e.g. Strawberry Perl or ActiveState.

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EXAMPLE CALLS:

1 - STANDARD CASE:
perl pincis.pl --fasta E-coli.fasta --peptides PICS_list.csv --enzyme Trypsin

Parse in the peptides from "PICS_list.csv" and work against the E-coli.fasta
database file which was digested with trypsin.

2 - EXOTIC CASE:
perl pincis.pl -f Arabidopsis.fasta -p Peptides.txt -e GluC -o MY_PICS_ANALYSIS

Takes the peptides from Peptides.txt and inferres the cleavage windows from
the Arabidopsis.fasta database, taking into account that the library was
digested with GluC and puts all the resulting files into the folder named
MY_PICS_ANALYSIS. If you do not supply an output directory, a default directory
named PINCIS_Output will be created.

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COMMAND-LINE ARGUMENTS:

	--fasta			FASTA file (def. "E-coli.fasta")
	--enzyme		Digestion enzyme [T]rypsin (def.), [G]luC, [L]egumain or [C]hymotrypsin
	--output-dir	Output directory (def. "PINCIS_Output_2020-9-9_11-53")
	--peptides		PICS peptide list (newline-separated)
	--replace		Replace all cutting chars for T/G/L/C enzymes
	--version		Version information
	--help			Short usage primer