Obtaining clean and informative mass spectra from complex chromatographic and high-resolution all-ions-fragmentation...

Area of Science:

• Analytical Chemistry
• Chemometrics
• Environmental Science

Background:

• Resolving co-eluting compounds in complex chromatography-mass spectrometry data is a significant analytical challenge.
• Data-independent acquisition techniques like mass spectrometry E (MS^E) generate complex datasets requiring advanced processing.
• Existing methods struggle with overlapping signals, limiting compound identification and quantification.

Purpose of the Study:

• To develop and validate a novel workflow for resolving co-eluting compounds in ultra-high pressure liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS^E) data.
• To assess the efficacy of nonnegative Parallel Factor Analysis 2 (NN-PARAFAC2) for improving mass spectral selectivity in data-independent acquisition.
• To apply the workflow to real-world environmental samples, including plant, soil, and water.

Main Methods:

• A workflow was developed utilizing a nonnegative Parallel Factor Analysis 2 (NN-PARAFAC2) algorithm.
• The workflow was applied to UHPLC-HRMS^E datasets from plant, soil, and water samples from a crop field study.
• NN-PARAFAC2 models were fitted to chromatographic intervals of spiked standards in both high-energy (HE) and low-energy (LE) MS^E acquisition modes.

Main Results:

• The NN-PARAFAC2 workflow successfully resolved 13 out of 14 spiked standards in plant and soil samples, even with co-elution.
• Mass spectral loadings from the NN-PARAFAC2 models could be matched to reference spectra for resolved compounds.
• Resolution was less effective in water samples due to a higher chromatographic baseline contributing to noisier data, with only seven standards resolved.

Conclusions:

• The presented workflow offers improved mass spectral selectivity for data-independent acquisition compared to using raw mass spectra.
• NN-PARAFAC2 effectively resolves co-eluting compounds, enabling accurate matching of fragment ions (HE trace) and precursor/adduct ions (LE trace).
• The workflow demonstrates potential for analyzing complex environmental samples, though performance may be impacted by data quality.