How to use the PICS

helmetpastoralΛογισμικό & κατασκευή λογ/κού

13 Δεκ 2013 (πριν από 3 χρόνια και 10 μήνες)

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How to use the
PICS
Perl computer script “PICS.pl”


The PICS Perl script takes a list of prime
-
side cleavage product, automatically retrieves the
corresponding non
-
prime side sequences and reconstructs the peptidic substrate. The Perl
computer script gener
ates two output files, PICS
-
consensus.csv and
PICS
-
preceeding
-
all
-
hits.csv
. Non
-
prime residues are recorded up to the first potential cleavage site of the
digestion protease. Most prime
-
side cleavage products can originate from several different
proteins.
PICS
-
preceeding
-
all
-
hits.csv lists the corresponding non
-
prime sequence for every
occurrence. This list is rendered non
-
redundant in
PICS
-
consensus.csv and this file also
accounts for potential ambiguity of non
-
prime residues

a
s discussed in the PICS resea
rch
paper (Schilling & Overall, Nature Biotechnology 2008).


The Perl computer script is a command line utility and requires installation of Perl. For Mac
OS X, Linux and cygwin, Perl is usually pre
-
installed. For Windows, Perl can be obtained
free (
http:/
/www.activestate.com/Products/activeperl/
). We recommend to create a dedicated
folder to run the PICS Perl script; the path to this folder should not contain spaces or special
characters. An example for Windows is
C:
\
PICS
-
analysis
\
. The PICS Perl script
r
equires a local copy of an IPI
-
style proteome database that corresponds to the organism
used for library generation. IPI
-
style proteome databases can be downloaded at
http://www.ebi.ac.uk/IPI/IPIhelp.html
. In addition, a list of prime
-
side cleavage product
s
should have been filtered with the PICS analysis EXCEL worksheet (tab 1), copied to a non
-
formatting text editor such as Notepad (Windows) or TextEdit (Mac OS) and saved in the
same folder as the PICS Perl script. All three files (PICS perl script, IPI
-
s
tyle proteome
database and list of prime sequences) should be present in the same folder.


At a command line (“Command Prompt” in Windows; “Terminal” in Mac OS X), the PICS Perl
script is started by typing
perl PICS.pl
. If the script is called without furt
her options, a
short help text is displayed. The required command line options are (in sequential order):

1)

list of prime sequences from PICS experiment, copied from tab 1 of the PICS EXCEL
worksheet and saved in a non
-
formatting text editor

2)

IPI
-
style prote
ome database

3)

Digestion protease used to generate library: (T)rypsin, (C)hymotrypsin or (G)luC.


Example:
perl PICS.pl MMP2.txt ipi
-
human.fasta T



In this example, the prime
-
side sequences are saved in a file called MMP2.txt. Please note
that this is
not

the original MASCOT output but that this sequence list was filtered using the
PICS EXCEL worksheet as described above. The file for the IPI style proteome is ipi
-
human.fasta and trypsin (“T”) was used to generate the peptide library.


For customization,
the PICS Perl script, like any other Perl script, can be edited with any text
editor.


Please do not hesitate in contacting us for any questions.


Prof. C. Overall (
chris.overall@ubc.ca)

Dr. O. Schilling (oschilling@gmail.com)