Library assessment with DIALib-QC

DIALib-QC v1.2 is a tool that allows users to analyze DIA libraries in a variety of formats including PeakView, OpenSWATH, Spectronaut and Predicted ion libraries (from Prosit- Spectronaut compatible generic format in csv) based on a library characteristics.

These include charge, length, retention time, m/z, complexity, etc. In addition to assessment, users can correct the ion library for any mass error and/or remove conflict assays. The supported libraries can be assessed online at SWATHAtlas for moderately-sized libraries (up to 200 MB), otherwise a downloaded version can be run locally on most Linux systems.

Download and Installation

The DIALib-QC v1.2 tool is written in the perl programming language, so perl installation is a pre-requisite on your Linux system. There is one non-core module dependency, 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 at available at the README file below. Once you've downloaded the script, you can execute the file directly, or as an argument to perl.

Files

README file

DIALib-QC v1.2 tool

DIALib-QC plotting tool

DIALib-QC Github

License

License file

COPYING file

Workflow

Below is the DIALib-QC v1.2 usage protocol or workflow to assess and repair a spectral ion library. The current version of the DIALib-QC supports the following list of modifications (modification annotation patterns).

Demo / Tutorial

Here we present a spectral ion library (K562_q3bad_PV) referring from the Midha et. al. paper published in Nature Communications (2020).

All the below mentioned steps work well with PeakView, Spectronaut, OpenSWATH and In-silico predicted library (from Prosit- generic csv (Spectronaut compatible)) formats. We are providing examples of two spectral ion libraries format (PeakView and In-silico ion library), SWATH_definitions, peptide mapping file and expected result files via the links below.

Tutorial: Steps to run DIALib-QC and add user defined modification (pdf)

Demo Input Files For PeakView, Spectronaut, OpenSWATH:

K562_q3bad_PV.txt

SWATHS definitions(optional)

Peptide to protein mapping(optional)

For In-silico predicted library:

HeLa_ce28.prosit.library.csv

Demo Output Files For PeakView, Spectronaut, OpenSWATH:

K562_q3bad_PV QC report

Mz_corrected new library

Mz_corrected new library QC report

Clean new library

Clean new library QC report

Graphical plots of Clean library

For In-silico predicted library:

QC report

Mass corrected library

Graphical plots of library (mass corrected)

Publication

Midha MK, Campbell DS, Kapil C, Kusebauch U, Hoopmann MR, Bader SL, Moritz RL. DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics. Nat Commun. 2020 Oct 16;11(1):5251.

doi: 10.1038/s41467-020-18901-y

PMID: 33067471

PMCID: PMC7567827