Library assessment with DIALib-QC
DIALib-QC is a tool that allows users to analyze DIA libraries in a variety of formats (PeakView, OpenSWATH, Spectonaut) based on a host of properties. These include charge, length, retention time, m/z, complexity, etc. This tool can be run online at PeptideAtlas for moderately-sized libraries (up to 200 MB), or downloaded and run locally on most *nix systems.
You can download the DIALib-QC tool by clicking here . It is written in the perl programming languange, so you will need to have perl installed on your *nix system in order to run it.
There is one non-core module dependency, Statistics::Regression, you can read more about it here . 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 at the bottom of this page. Once you've downloaded the script, you can execute the file directly, or as an argument to perl:
perl assess_swathlib.pl --help
Usage: assess_swathlib.pl --ion_library libfile [ --peptide_file pepfile ] > output_file.tsv
alt_decoy Alternate decoy prefix (default is DECOY)
assess_massdiff Compute difference between library masses and theoretical values
c, coldefs print out column definitions
h, help Print this usage information and exit
i, ion_library Path to ion library file in Peakview/OpenSWATH/Spectronaut format (required)
peptide_file Path to peptide digest file, format is protein(s) peptide
print_mismatch Print out ions whose m/z values differ significantly from theoretical
v, verbose Verbose output mode
show_mods Print list of mass modifications seen in library
skip_decoys Skip DECOY entries when computing statistics
swath_file Path to file of SWATH definitions, format min_m/z max_m/z
print_ux Print unexplained proteins (seen in ion library but not in peptide_file if provided
write Write MGF file with info from each spectrum (rare)
As shown in the example above, it is generally useful to redirect the output to a file (TSV) for later viewing. We've provided examples of the SWATH_definitios and peptide mapping files via the links below:
Peptide to protein mapping
You can install the Statistics::Regression module either a) manually or b) 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.
a) Manual installation of Statistics::Regression
tar xvfz Statistics-Regression-0.53.tar.gz
perl Makefile.PL [ --PREFIX="/path/to/user_lib_dir/" ]
[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/ ]
b) CPAN installation of Statistics::Regression
[sudo] perl -MCPAN -e shell
cpan> install Statistics::Regression