Shinyscreen

Shinyscreen facilitates initial exploration and prescreening of raw liquid chromatography–high-resolution mass spectrometry (LC-HRMS) data to support suspect screening and identification of organic pollutants, including pesticides and transformation products (TPs).

Key Features:

• Raw Data Visualization: Generates unprocessed MS1 and MS2 chromatograms and corresponding MS2 spectra for specified target masses from raw LC-HRMS files.
• Prescreening Aid: Implements built-in prescreening to assess spectral quality for preliminary evaluation of MS data.
• Automated Workflow Integration: Integrates automated quality control steps and spectral annotation within computational workflows for LC-HRMS analysis.
• Suspect List Creation and Retrieval: Supports creation and retrieval of suspect lists focused on chemical classes such as pesticides, incorporating entries from multiple languages and sources.
• Transformation Product Analysis: Enables automated retrieval of transformation products from databases such as PubChem to support analysis of parent compounds and derivatives.

Scientific Applications:

• Environmental suspect screening: Detection and characterization of pesticides and their transformation products in environmental samples using LC-HRMS MS1/MS2 data.
• Case study — Luxembourgish rivers: Applied to river samples where analyses revealed 162 potential pesticide masses, 135 potential TP masses, and 31 compounds confirmed at Level-1 confidence.

Methodology:

Inputs are raw LC-HRMS data files and lists of target masses; the package generates MS1 and MS2 chromatograms and MS2 spectra, applies prescreening for spectral quality assessment, and integrates with custom scripts and open-source tools such as MetFrag and PubChem retrieval for downstream annotation and identification.