DIALib-QC v1.1 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" - Perl version 5.30.0 on Linux: Ubuntu 20.04 2)Installation guide DIALib-QC v1.1 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' (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 v1.1 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 .