AutoChrom: Processing Best Practices

Autonomous Processing Configuration

Detector Lag Calibration: Calculate and apply the detector lag (time offset between UV and MS signals) prior to initiating LC/UV/MS batch processing to ensure accurate cross-detector alignment.

• Avoid carrying over settings from previous projects when creating new workflows unless there is a specific reason to reuse them. To ensure a clean setup, disable Prefer Previously Used Settings.
• Enable Preserve Existing IntelliXtract Results only when you intentionally want to reuse previously generated results. Otherwise, disable this option to ensure all data are processed from scratch.
• Use Bypass Already Processed Signals and Skip Processing if Optional carefully. While these options can improve processing efficiency, they may prevent necessary reprocessing when methods, parameters, or source data have changed.

LCMS vs. LCUV Processing Workflows

• LCMS workflows typically involve running IntelliXtract, followed by peak picking and peak matching. Compound detection relies on mass spectral information and ion extraction.
• LCUV workflows generally require peak picking and peak matching only. Detection is based on UV chromatographic and spectral data.

Peak Matching Options

When detecting, aligning, and comparing chromatographic peaks across multiple datasets, consider the following settings and best practices:

• Retention Time (RT) Matching Window: Adjust retention time matching tolerances and abundance thresholds to accommodate retention time shifts, peak variability, and co-eluting components.
• Mass Tolerance & Isotopic Pattern Matching (MS): Match components using exact mass (m/z within specified x{ppm} or y{Da} tolerances) and confirm matches using isotopic abundance profiles or adduct filters.
• Review any unmatched or ambiguously matched peaks. Although automated processing can significantly accelerate getting results, manual verification may still be necessary for complex samples and challenging separations.

• Matching Score / Occurrence Threshold: Set an appropriate threshold to define the minimum number (or percentage) of experiments in which a peak must be detected. Setting this too strictly—such as requiring a component to appear in all experiments—may filter out critical sample-specific impurities, degradants, or low-abundance peaks of interest.

UV Peak Purity and Quality Assessment

• Peak purity evaluates the spectral consistency across a chromatographic peak, including the apex and peak edges, helping identify potential co-eluting components.

• Peak quality measures spectral stability and noise characteristics across the entire peak profile.