Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?

Fenaille, François; Saint-Hilaire, Pierre Barbier; Rousseau, Kathleen; Junot, Christophe

doi:10.1016/j.chroma.2017.10.043

Cited by 108 publications

(72 citation statements)

References 110 publications

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“…Because of these major challenges faced for non‐targeted metabolome assessment, employment of additional analytical selectivity via the use of high‐resolution fragment (HR MS/MS) spectra can be used to support metabolite identification as a complementary and chemically informative descriptor . In the case of HR MS/MS, data‐dependent acquisition strategies rely on isolation and fragmentation of precursor ions which have exceeded a user‐defined intensity threshold or any other measurable criteria such as isotopologue pattern, mass defect or the presence of a diagnostic ion . However, some limitations for non‐targeted assessment are also apparent.…”

Section: Introductionmentioning

confidence: 99%

Rapid screening methods for yeast sub‐metabolome analysis with a high‐resolution ion mobility quadrupole time‐of‐flight mass spectrometer

Mairinger

Kurulugama

Causon

et al. 2019

Rapid Comm Mass Spectrometry

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Rationale The wide chemical diversity and complex matrices inherent to metabolomics still pose a challenge to current analytical approaches for metabolite screening. Although dedicated front‐end separation techniques combined with high‐resolution mass spectrometry set the benchmark from an analytical point of view, the increasing number of samples and sample complexity demand for a compromise in terms of selectivity, sensitivity and high‐throughput analyses. Methods Prior to low‐field drift tube ion mobility (IM) separation and quadrupole time‐of‐flight mass spectrometry (QTOFMS) detection, rapid ultrahigh‐performance liquid chromatography separation was used for analysis of different concentration levels of dansylated metabolites present in a yeast cell extract. For identity confirmation of metabolites at the MS2 level, an alternating frame approach was chosen and two different strategies were tested: a data‐independent all‐ions acquisition and a quadrupole broad band isolation (Q‐BBI) directed by IM drift separation. Results For Q‐BBI analysis, the broad mass range isolation was successfully optimized in accordance with the distinctive drift time to m / z correlation of the dansyl derivatives. To guarantee comprehensive sampling, a broad mass isolation window of 70 Da was employed. Fragmentation was performed via collision‐induced dissociation, applying a collision energy ramp optimized for the dansyl derivatives. Both approaches were studied in terms of linear dynamic range and repeatability employing ethanolic extracts of Pichia pastoris spiked with 1 μM metabolite mixture. Example data obtained for histidine and glycine showed that drift time precision (<0.01 to 0.3% RSD, n = 5) compared very well with the data reported in an earlier IM‐TOFMS‐based study. Conclusions Chimeric mass spectra, inherent to data‐independent analysis approaches, are reduced when using a drift time directed Q‐BBI approach. Additionally, an improved linear dynamic working range was observed, representing, together with a rapid front‐end separation, a powerful approach for metabolite screening.

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Section: Introductionmentioning

confidence: 99%

Rapid screening methods for yeast sub‐metabolome analysis with a high‐resolution ion mobility quadrupole time‐of‐flight mass spectrometer

Mairinger

Kurulugama

Causon

et al. 2019

Rapid Comm Mass Spectrometry

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“…As a consequence, AIF and MS(E) are affected by the same acquisition‐linked limitations. The high complexity of AIF spectra is significantly reduced by utilizing MS(E) . It was, however, noted that AIF, and with this MS(E), spectra frequently show low ion abundance .…”

Section: Resultsmentioning

confidence: 99%

“…The high complexity of AIF spectra is significantly reduced by utilizing MS(E). 20,21 It was, however, noted that AIF, and with this MS(E), spectra frequently show low ion abundance. 22 This is probably due to the large number of precursor ions in the collision chamber and to ion transmission losses when handling a large mass range instead of a narrow unit mass range.…”

Section: Benefits Of Using Mass Isolation-based Acquisition Modesmentioning

confidence: 86%

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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“…To address this issue of ion species redundancy, additional data processing steps are required before assigning any feature to a given metabolite: (a) a grouping step where related features (ie, ion peaks arising from the same compound) are clustered, (b) a single metabolite feature most often corresponding to a protonated or deprotonated ion is selected on the basis of the interpretation of the mass spectrum, and (c) is used to search mass spectral databases created from a collection of spectral data obtained from reference compounds analyzed under similar conditions. The compound candidates are tentatively identified by tandem mass spectrometry following reinjection(s) into the LC‐MS/MS system using targeted MS/MS workflows . Such a procedure is highly tedious as well as time‐consuming and sample‐consuming, while its completeness relies essentially on analyst manual data analysis.…”

Section: Introductionmentioning

confidence: 99%

“…The compound candidates are tentatively identified by tandem mass spectrometry following reinjection(s) into the LC-MS/MS system using targeted MS/MS workflows. 9 Such a procedure is highly tedious as well as time-consuming and sampleconsuming, while its completeness relies essentially on analyst manual data analysis. The quest for an identification of metabolites as complete and accurate as possible has led to an increasing development of shared and public mass spectral databases (including LC-MS and MS/MS data) concomitantly with bioinformatic tools expansion (eg, spectral signal matching software, quantitative structure-retention relationship, spectral similarity network, etc).…”

mentioning

confidence: 99%

Proposal for a chemically consistent way to annotate ions arising from the analysis of reference compounds under ESI conditions: A prerequisite to proper mass spectral database constitution in metabolomics

et al. 2019

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Nowadays, high‐resolution mass spectrometry is widely used for metabolomic studies. Thanks to its high sensitivity, it enables the detection of a large range of metabolites. In metabolomics, the continuous quest for a metabolite identification as complete and accurate as possible has led during the last decade to an ever increasing development of public MS databases (including LC‐MS data) concomitantly with bioinformatic tool expansion. To facilitate the annotation process of MS profiles obtained from biological samples, but also to ease data sharing, exchange, and exploitation, the standardization and harmonization of the way to describe and annotate mass spectra seemed crucial to us. Indeed, under electrospray (ESI) conditions, a single metabolite does not produce a unique ion corresponding to its protonated or deprotonated form but could lead to a complex mixture of signals. These MS signals result from the existence of different natural isotopologues of the same compound and also to the potential formation of adduct ions, homomultimeric and heteromultimeric ions, fragment ions resulting from “prompt” in‐source dissociations. As a joint reflection process within the French Infrastructure for Metabolomics and Fluxomics (MetaboHUB) and with the purpose of developing a robust and exchangeable annotated MS database made from pure reference compounds (chemical standards) analysis, it appeared to us that giving the metabolomics community some clues to standardize and unambiguously annotate each MS feature was a prerequisite to data entry and further efficient querying of the mass spectral database. The use of a harmonized notation is also mandatory for interlaboratory MS data exchange. Additionally, thorough description of the variety of MS signals arising from the analysis of a unique metabolite might provide greater confidence on its annotation.

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Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand?

Cited by 108 publications

References 110 publications

Rapid screening methods for yeast sub‐metabolome analysis with a high‐resolution ion mobility quadrupole time‐of‐flight mass spectrometer

Rapid screening methods for yeast sub‐metabolome analysis with a high‐resolution ion mobility quadrupole time‐of‐flight mass spectrometer

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

Proposal for a chemically consistent way to annotate ions arising from the analysis of reference compounds under ESI conditions: A prerequisite to proper mass spectral database constitution in metabolomics

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