Comparison of data acquisition modes with Orbitrap high‐resolution mass spectrometry for targeted and non‐targeted residue screening in aquacultured eel

Abstract

Rationale A current trend in monitoring chemical contaminants in animal products is to use high‐resolution mass spectrometry (HRMS). In this study, several HRMS data acquistion modes using Orbitrap MS for simultaneous full‐scan MS in combination with MS2 analysis were evaulated for their effectiveness in detecting and identifying both targeted and non‐targeted veterinary drug residues in aquacultured eel samples. Methods Sample preparation consisted of an acidic acetonitrile extraction with solid‐phase extraction cleanup for analysis using LC/HRMS. Different data acquisition methods, including full‐scan MS with non‐targeted all ion fragmentation (AIF), multiplexed or variable data‐independent analysis (mDIA or vDIA), targeted data‐dependent MS2 (DDMS2), and parallel reaction monitoring (PRM) acquisition, were explored. The methods were evaluated with fortified eel tissue and imported eel samples to determine how many analytes could be detected and identified. Results For non‐targeted data acquisition, the number of analytes detected using DIA methods matched the results obtained by AIF, but the resulting product ion scans were more diagnostic because characteristic ions were predominant in the DIA MS2 spectra. In targeted analysis for a limited list of 68 compounds, full‐scan MS followed by PRM was advantageous compared with DDMS2 because high‐quality MS2 spectra were generated for almost all the analytes at target testing levels. Conclusions For residue screening, AIF has fast MS1 scan speed with adequate detection of product ions but may lead to false positive findings. DIA methods are better suited to monitor for both targeted and non‐targeted compounds because they generate more characteristic MS2 spectra for retrospective library searching. For follow‐up targeted analysis, PRM is prefered over DDMS2 when searching for a limited set of compounds.

Comparison of Full-Scan, Data-Dependent, and Data-Independent Acquisition Modes in Liquid Chromatography–Mass Spectrometry Based Untargeted Metabolomics

“…Among the limitations of the present study is the limited choice of LC-MS combinations. We focused on the most commonly used combinations in LC-MS based metabolomics (e.g., RP­(+) and HILIC(−)), which is also common practice in other MS method comparison works. ,− Researchers who want to check their specific LC-MS methods can follow our workflow to perform their comparison. Furthermore, the parameters for LC-MS analysis and data processing have been considered optimized, yet the choice is fairly subjective.…”

Re-Examining the Impact of Minimal Scans in Liquid Chromatography–Mass Spectrometry Analysis

“…Besides, the high-resolution power permits analysis efficiency as little time is needed for the method development and optimization compared to MRM in which tuning is required per compound . Moreover, the capability of simultaneously acquiring full scan (MS) and MS/MS (MS 2 ) of the most intense precursor ion with a scan mode called data-dependent acquisition (DDA) enables the quantitation of a parent ion and structure elucidation for metabolites during the same MS acquisition. Because of the advantaged features above, the HRMS application is rather versatile, which includes but is not limited to untargeted and targeted metabolomics and proteomics analysis, , absolute quantitation analysis (environmental and toxicological substances analysis, small pharmaceutical molecules and large peptides, and pharmacokinetics study), ,− and semiquantitative analysis (ADME (absorption, distribution, metabolism, and excretion) studies, metabolites profiling, biotransformation, and identification (MetID). , …”

Applications of nDATA for screening, quantitation, and identification of pesticide residues in fruits and vegetables using UHPLC/ESI Q‐Orbitrap all ion fragmentation and data independent acquisition

“…AIF has advantages of faster scan rates or shorter cycle times at higher resolution settings, but it is less selective for identifying analytes because the acquired MS/MS spectra include all fragment ions in the entire mass range. On the contrary, although it has a longer cycle time, DIA generates higher quality MS/MS spectra because of narrower isolation mass windows which could allow for more in‐depth mass library or compound database searching for screening or identification 31 . However, an advanced Q‐Orbitrap with faster scanning speed than the Q Exactive platform will benefit from a narrower isolation window for selectivity and speed 24 …”

“…On the contrary, although it has a longer cycle time, DIA generates higher quality MS/MS spectra because of narrower isolation mass windows which could allow for more in-depth mass library or compound database searching for screening or identification. 31 However, an advanced Q-Orbitrap with faster scanning speed than the Q Exactive platform will benefit from a narrower isolation window for selectivity and speed. 24 Figure 1 shows the parameter settings of both full MS/vDIA and AIF.…”