Coalescence and self‐bunching observed in commercial high‐resolution mass spectrometry instrumentation

Kaufmann, Anton; Walker, Stephen

doi:10.1002/rcm.8054

Cited by 18 publications

(10 citation statements)

References 28 publications

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“…The level of background ion signal plays a central role in determining the sensitivity of LC-MS analyses, in particular for screening assays, by negatively impacting the overall analytical performance due to the finite intra-scan dynamic range and possible coalescence and self-bunching effects (Kaufmann and Walker, 2017, 2018). In the context of our methodology, an Orbitrap detector has a finite ion capacity and therefore the length of time (ion injection time) ions are collected for analysis is tightly regulated by setting a target ion number (automated gain control setting).…”

Section: Discussionmentioning

confidence: 99%

Targeted High Resolution LC/MS3 Adductomics Method for the Characterization of Endogenous DNA Damage

et al. 2019

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DNA can be damaged through covalent modifications of the nucleobases by endogenous processes. These modifications, commonly referred to as DNA adducts, can persist and may lead to mutations, and ultimately to the initiation of cancer. A screening methodology for the majority of known endogenous DNA adducts would be a powerful tool for investigating the etiology of cancer and for the identification of individuals at high-risk to the detrimental effects of DNA damage. This idea led to the development of a DNA adductomic approach using high resolution data-dependent scanning, an extensive MS2 fragmentation inclusion list of known endogenous adducts, and neutral loss MS3 triggering to profile all DNA modifications. In this method, the detection of endogenous DNA adducts is performed by observation of their corresponding MS3 neutral loss triggered events and their relative quantitation using the corresponding full scan extracted ion chromatograms. The method's inclusion list consists of the majority of known endogenous DNA adducts, compiled, and reported here, as well as adducts specific to tobacco exposure included to compare the performance of the method with previously developed targeted approaches. The sensitivity of the method was maximized by reduction of extraneous background signal through the purification and minimization of the amount of commercially obtained enzymes used for the DNA hydrolysis. In addition, post-hydrolysis sample purification was performed using off-line HPLC fraction collection to eliminate the highly abundant unmodified bases, and to avoid introduction of plasticizers found in solid-phase extraction cartridges. Also, several instrument parameters were evaluated to optimize the ion signal intensities and fragmentation spectra quality. The method was tested on an animal model of lung carcinogenesis where A/J mice were exposed to the tobacco specific lung carcinogen 4-methylnitrosamino-1-3-pyridyl-1-butanone (NNK) with its effects enhanced by co-exposure to the pro-inflammatory agent lipopolysaccharide (LPS). Lung DNA were screened for endogenous DNA adducts known to result from oxidative stress and LPS-induced lipid peroxidation, as well as for adducts due to NNK exposure. The relative quantitation of the detected DNA adducts was performed using parallel reaction monitoring MS2 analysis, demonstrating a general workflow for analysis of endogenous DNA adducts.

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Section: Discussionmentioning

confidence: 99%

Targeted High Resolution LC/MS3 Adductomics Method for the Characterization of Endogenous DNA Damage

et al. 2019

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“…In contrast, when mixture VI , analyzed with direct MS 2 , is processed, only 4 of 6 molecular formulae and 2 of 6 structures are correct. The wrong assignment of the molecular formulae arises from a combination of two adverse effects in high‐resolution tandem MS: (1) partial ion coalescence 45 , 46 , 47 leads to significant shifts in accurate mass of the precursor (Figure S13 , supporting information) and (2) the many fragments from other precursors possibly coincided with a fragment which would be consistent with the erroneous precursor mass. Here, IQAROS can help by eliminating fragments which coincidently fit a reasonable mass difference but actually stem from an interfering precursor.…”

Section: Resultsmentioning

confidence: 99%

Resolving isobaric interferences in direct infusion tandem mass spectrometry

Kaeslin

Zenobi

2022

Rapid Comm Mass Spectrometry

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Rationale The co‐fragmentation of precursors in direct infusion (DI) tandem high‐resolution mass spectrometry (HRMS) can complicate the fragment spectra and consequently lead to false hits during compound identification. Methods The method herein described, termed IQAROS (incremental quadrupole acquisition to resolve overlapping spectra), modulates the intensities of precursors and fragments by stepwise movement of the quadrupole isolation window over the mass‐to‐charge (m/z) range of the precursors. The modulated signals are then deconvoluted by a linear regression model to reconstruct the fragment spectra with less interference. The hardware to demonstrate the use of IQAROS was an orbitrap with electrospray ionization (ESI) or secondary electrospray ionization (SESI), although the method can also be applied to other ionization techniques or mass analyzers. Results Assessing the performance of IQAROS with isobaric standards revealed that the reconstructed fragment spectra match with spectra acquired from the pure standards and that more compounds were correctly identified compared with the classical approach with the quadrupole centered at the m/z value of the precursor of interest. Moreover, the strength of IQAROS is exemplified by the identification of two isobaric biomarkers directly from a breath sample with SESI‐HRMS. Conclusions With IQAROS, cleaner fragment spectra of co‐fragmenting isobars during DI‐HRMS analysis can be obtained. IQAROS can easily be set up by the standard graphical user interface of the instrument. Therefore, it facilitates the characterization of features of interest in samples analyzed by DI‐HRMS, for example, in high‐throughput or real‐time metabolomics.

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“…The thus obtained wrong “accurate” mass is in many cases the ion‐abundance weighted average of the two correct “accurate” (exact) masses. In addition, there is the phenomenon of coalescence where two isobaric ion populations behave like a single ion population and the resulting mass peak appears as a perfect symmetrical shape. The sequential isolation of mass ranges (SWATH windows) reduces the density (complexity) of the product ion spectra.…”

Section: Resultsmentioning

confidence: 99%

Partially overlapping sequential window acquisition of all theoretical mass spectra: A methodology to improve the spectra quality of veterinary drugs present at low concentrations in highly complex biological matrices

Kaufmann¹,

Maden²,

Walker³

2020

Rapid Comm Mass Spectrometry

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Rationale Residues of veterinary drugs in food matrices have to be detected, identified and confirmed at low concentrations. Data‐independent acquisition (DIA) methods such as the sequential window acquisition of all theoretical spectra (SWATH) permit the extraction of relatively clean spectra out of complex matrices. Such spectra can be significantly improved by using a modified SWATH algorithm which provides several times narrower mass isolation windows without affecting the cycle time. Methods A quadrupole‐time‐of‐flight mass spectrometer was operated in a partially overlapping SWATH mode. Unlike in conventional SWATH, acquisition sequences are not identically repeated, but each sequence is initiated with a mass intercept (mass shift). Pearson correlation is used to assign HRMS‐resolved product ions to the precursor mass of interest. Trace analytes (veterinary drugs) in a complex matrix extract (bovine liver) were investigated. Results Utilizing identical cycle times, the partially overlapping SWATH mode produced for the investigated small molecules a significantly higher selectivity than the conventional SWATH acquisition mode. The acquisition strategy enables long ion accumulation times and therefore the required high sensitivity of detection. The study investigates the quality of the obtained product ion spectra and compares it with that in conventional acquisition modes. Conclusions The modified SWATH mode permits high duty cycles in combination with narrow virtual mass windows. The technique is a further step toward harvesting a HRMS product ion spectrum out of a data‐independent acquisition which moves closer towards the quality of a dedicated precursor unit isolation product ion spectrum.

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Coalescence and self‐bunching observed in commercial high‐resolution mass spectrometry instrumentation

Cited by 18 publications

References 28 publications

Targeted High Resolution LC/MS3 Adductomics Method for the Characterization of Endogenous DNA Damage

Targeted High Resolution LC/MS3 Adductomics Method for the Characterization of Endogenous DNA Damage

Resolving isobaric interferences in direct infusion tandem mass spectrometry

Partially overlapping sequential window acquisition of all theoretical mass spectra: A methodology to improve the spectra quality of veterinary drugs present at low concentrations in highly complex biological matrices

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