DIALib-QC, an assessment tool for the systematic evaluation of spectral assay libraries to improved data independent acquisition analysis.
DIALib-QC v1.0 Tool to assess the spectral ion libraries of PEAKVIEW,SPECTRONAUT or OPENSWATH formats.
1)System Requirements:
- Perl 5 version 16 on Linux systems
- Perl Statistics::Regression module dependency (recommended)
- Perl Statistics::R module dependency (recommended)
- R libraries: ggplot2, scales, ggpubr
Tool successfully tested on
- Windows 10 Enterprise
- Oracle Linux Server release 7.7 VERSION="7.7"
2)Installation guide
DIALib-QC v1.0 is a tool that allows users to analyze DIA libraries in a variety of formats (PeakView, OpenSWATH, Spectonaut and Prosit) based on a host of properties.
These include charge, length, retention time, m/z, complexity, etc. This tool can be run online at PeptideAtlas(https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/AssessDIALibrary)
for moderately-sized libraries (up to 200 MB). The tool provides an option to download the result as tabular format and a single pdf file containing plots of library characterstics. It is written in the perl programming language, so you will need to have perl
installed on your Linux system in order to run it. For ploting feature, R installation along with few libraries is a pre-requisite.
You can downloaded DIALib-QC tool at http://www.swathatlas.org/DIALibQC.php link and run the tool locally on most Linux systems.
(A) Installing Instructions LINUX
There is one non-core module dependency, Statistics::Regression, you can read more about it at (https://metacpan.org/pod/Statistics::Regression).
The tool will work without it, but you will lose the test comparing RT values of +2 and +3 ions of the same modified peptide, a metric of the retention time
consistency of the ion library being analyzed.
Instructions for perl module installation are as follows:
You can install the Statistics::Regression module either
i) manually or ii) via CPAN, as shown below Optional components in [ square brackets ],
sudo allows user to install as if root (probably required for system-wide installations),
while --PREFIX allows user to designate an alternative library location on which they have write permissions.
i) Manual installation of Statistics::Regression
wget "https://cpan.metacpan.org/authors/id/I/IA/IAWELCH/Statistics-Regression-0.53.tar.gz"
tar xvfz Statistics-Regression-0.53.tar.gz
cd Statistics-Regression-0.53/
perl Makefile.PL [ --PREFIX="/path/to/user_lib_dir/" ]
make
[sudo] make install
If doing a custom PREFIX install, you'll need to insure that the library can be found, e.g.
[ export PERL5LIB=$PERL5LIB:/path_to_user_lib_dir/share/perl5/ ]
ii) CPAN installation of Statistics::Regression
[sudo] perl -MCPAN -e shell
cpan[2]> install Statistics::Regression
exit
You can install the Statistics::R module as
i) perl -MCPAN -e 'install Statistics::R'
You also need to install ggplot2 and ggpubr in R consule
install.packages("ggplot2")
install.packages("ggpubr"）
(B) Usage after installation: Assessing Library
perl assess_swathlib.pl --help
Starting run
Missing required option ion_library
Usage: assess_swathlib.pl --ion_library libfile [ --peptide_file pepfile --output output_file ]
# Required
ion_library Path to ion library file in Peakview/OpenSWATH/Spectronaut/Prosit format (required)
# Commonly used
assess_massdiff Compare library masses to theoretical monoisotopic values
c, coldefs print out column definitions
f, full_stats Print file (output_file.fullstats)
h, help Print this usage information and exit
invert_output Invert output, 3 columns by X rows
o, output_file File (base) to which to write data; given MyOut, generates
MyOut.QC, MyOut.fullstats, etc. If not specified, library name
is used.
peptide_file Path to peptide digest file, format is protein(s) peptide
swath_file Path to file of SWATH definitions, format min_m/z max_m/z
# Generate filtered/corrected library
correct_mz Will compute precursor and fragment masses for each entry
in library and print new library:
ion_library.mz_corrected
Requires use of --assess, precludes use of
filter_assays, rt_stats, full_stats, print_ux
filter_assays Assesses each assay, and removes any that have a
problem (m/z error, discrepancy from SWATH file).
Creates 2 new libraries, one with all passing assays and
another with all failed (problem) assays:
ion_library.clean
ion_library.problem
Requires use of --assess, precludes use of correct_mz,
rt_stats, full_stats, print_ux
# Other
alt_decoy Alternate decoy prefix (default is DECOY)
debug Print parsed/library values in case of format issues
print_mismatch Print out ions whose m/z values differ significantly from
theoretical
print_ux Print unexplained proteins (seen in ion library but not
in peptide_file if provided
rt_stats Print file of +2/+3 RTs for analysis to output_file.RT,
only if enough for regression
skip_decoys Skip DECOY entries when computing statistics
v, verbose Verbose output mode
write Write MGF file with info from each spectrum (rare)
zero_pad Print intermediate values=0 with full_stats.
(C) Usage after installation: Generating plots
Usage: DIALib-QC_RPlot.pl library.fullstats library.RT
or
Usage: DIALib-QC_RPlot.pl library.fullstats
(D) License Copyright (C) 2020 Moritz Lab, Institute for Systems Biology
DIALib-QC v1.0 program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.