Abstract
Tandem mass spectral databases are indispensable for fast and reliable compound identification in nontargeted analysis with liquid chromatography–high resolution tandem mass spectrometry (LC-HRMS/MS), which is applied to a wide range of scientific fields. While many articles now review and compare spectral libraries, in this manuscript we investigate two high-quality and specialized collections from our respective institutes, recorded on different instruments (quadrupole time-of-flight or QqTOF vs. Orbitrap). The optimal range of collision energies for spectral comparison was evaluated using 233 overlapping compounds between the two libraries, revealing that spectra in the range of CE 20–50 eV on the QqTOF and 30–60 nominal collision energy units on the Orbitrap provided optimal matching results for these libraries. Applications to complex samples from the respective institutes revealed that the libraries, combined with a simple data mining approach to retrieve all spectra with precursor and fragment information, could confirm many validated target identifications and yield several new Level 2a (spectral match) identifications. While the results presented are not surprising in many ways, this article adds new results to the debate on the comparability of Orbitrap and QqTOF data and the application of spectral libraries to yield rapid and high-confidence tentative identifications in complex human and environmental samples.
Highlights
Tandem mass spectral databases are indispensable for fast and reliable compound identification in nontargeted analysis with liquid chromatography–high resolution tandem mass spectrometry (LC-HRMS/MS) [1,2,3,4,5,6,7]
For the QqTOF spectra, fragmentation was accomplished by collision-induced dissociation (CID) at various collision energies
Out of the entire set of Orbitrap spectra, 321 spectra were acquired with CID at 35 nominal collision energy units (NCE)
Summary
Tandem mass spectral databases are indispensable for fast and reliable compound identification in nontargeted analysis with liquid chromatography–high resolution tandem mass spectrometry (LC-HRMS/MS) [1,2,3,4,5,6,7]. These databases have been applied in diverse fields, including forensics, environmental analysis, food analysis, and metabolomics. According to the scheme introduced by Schymanski et al [14], a Level 2a identification (probable structure via spectral match) can immediately be reached with sufficient match to a library spectrum. Even Level 1 (structure confirmed by a reference compound) can be achieved when the library spectrum and associated retention time (or index) match
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