Recognizing Contamination Fragment Ions in Liquid Chromatography–Tandem Mass Spectrometry Data

Tandem mass spectral (MS/MS) data in liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis are often contaminated as the selection of precursor ions is based on a low-resolution quadrupole mass filter. In this work, we developed a strategy to differentiate contamination fragment ions (CFIs) from true fragment ions (TFIs) in an MS/MS spectrum. The rationale is that TFIs should coelute with their parent ions, but CFIs should not. To assess coelution, we performed a parallel LC-MS/MS analysis in data-independent acquisition (DIA) with all-ion-fragmentation (AIF) mode. Using the DIA (AIF) data, peak-peak correlation (PPC) score is calculated between the extracted ion chromatogram (EIC) of the fragment ion using the MS/MS scans and the EIC of the precursor ion using the MS1 scans. A high PPC score is an indication of TFIs, and a low PPC score is an indication of CFIs. Tested using metabolomics data generated by high resolution QTOF and Orbitrap MS from various vendors in different LC-MS configurations, we found that more than 70% of the fragment ions have PPC scores < 0.8 and identified three common sources of CFIs, including (1) solvent contamination, (2) adjacent chemical contamination, and (3) undetermined signals from artifacts and noise. Combining PPC scores with other precursor and fragment ion information, we further developed a machine learning model that can robustly and conservatively predict CFIs. Incorporating the machine learning model, we created an R program, MS2Purifier, to automatically recognize CFIs and clean MS/MS spectra of metabolic features in LC-MS/MS data with high sensitivity and specificity.