Ultra-fast searching assists in evaluating sub-ppm mass accuracy enhancement in U-HPLC/Orbitrap MS data

Lommen, Arjen; Gerssen, Arjen; Oosterink, J. Efraim; Kools, Harrie J.; Ruiz‐Aracama, Ainhoa; Peters, Ruud; Mol, Hans

doi:10.1007/s11306-010-0230-y

Cited by 40 publications

(37 citation statements)

References 11 publications

(20 reference statements)

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“…Noteworthy, the average error was approximately zero around m/z 622.0289, the m/z of the compound used for lock-mass calibration. The m/z deviations depend on m/z value (Mihaleva et al, 2008;Lommen et al, 2011). We followed the plausible argument of the authors to assume that we must have correctly annotated a certain number of lipid sum formulae because they are known to exist in our sample.…”

Section: M/z Correctionmentioning

confidence: 99%

Structure Annotation and Quantification of Wheat Seed Oxidized Lipids by High-Resolution LC-MS/MS

2017

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Lipid oxidation is a process ubiquitous in life, but the direct and comprehensive analysis of oxidized lipids has been limited by available analytical methods. We applied high-resolution liquid chromatography-mass spectrometry (LC-MS) and tandem mass spectrometry (MS/MS) to quantify oxidized lipids (glycerides, fatty acids, phospholipids, lysophospholipids, and galactolipids) and implemented a platform-independent high-throughput-amenable analysis pipeline for the high-confidence annotation and acyl composition analysis of oxidized lipids. Lipid contents of 90 different naturally aged wheat (Triticum aestivum) seed stocks were quantified in an untargeted high-resolution LC-MS experiment, resulting in 18,556 quantitative mass-to-charge ratio features. In a posthoc liquid chromatography-tandem mass spectrometry experiment, high-resolution MS/MS spectra (5 mD accuracy) were recorded for 8,957 out of 12,080 putatively monoisotopic features of the LC-MS data set. A total of 353 nonoxidized and 559 oxidized lipids with up to four additional oxygen atoms were annotated based on the accurate mass recordings (1.5 ppm tolerance) of the LC-MS data set and filtering procedures. MS/MS spectra available for 828 of these annotations were analyzed by translating experimentally known fragmentation rules of lipids into the fragmentation of oxidized lipids. This led to the identification of 259 nonoxidized and 365 oxidized lipids by both accurate mass and MS/MS spectra and to the determination of acyl compositions for 221 nonoxidized and 295 oxidized lipids. Analysis of 15-year aged wheat seeds revealed increased lipid oxidation and hydrolysis in seeds stored in ambient versus cold conditions. Lipid oxidation is a process inevitably connected to life. Although essential for all respiring organisms, oxygen can form reactive species (ROS). The accumulation of these compounds leads to the phenomenon commonly referred to as oxidative stress in microbes and plant and animal tissues. ROS play a role in the attack against microbial pathogens by host cells (Imlay, 2013), time-dependent death of dormant seeds (Lee et al., 2010), human diseases (Coyle and Puttfarcken, 1993;Giugliano et al., 1996), in aging (Sohal and Weindruch, 1996;Sohal et al., 2002), and in signaling processes (Gilroy et al., 2016;Mignolet-Spruyt et al., 2016) Unlike oxidized fatty acids (FAs), oxidized lipids are hardly available commercially. Targeted liquid chromatography-mass spectrometry (LC-MS) analysis of oxidized lipids using authentic standards is not very common (Hui et al., 2010;Ravandi et al., 2014). Often, oxidized lipids are detected using tandem mass spectrometry (MS/MS), where the collision-induced products of precursor ions (PRs) are scanned for fragments or neutral losses (NLs) that correspond to oxidized acyl residues expected in oxidized lipids (Spickett and Pitt, 2015), and in some cases, higher resolution MS/MS spectra are provided to support the identification (Buseman et al., 2006;Vu et al., 2012).High-resolution mass spectrometry (MS) allows for ...

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Section: M/z Correctionmentioning

confidence: 99%

Structure Annotation and Quantification of Wheat Seed Oxidized Lipids by High-Resolution LC-MS/MS

2017

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“…Both q-TOF and Orbitrap mass analyzers generally have mass accuracies below 5 ppm [54][55][56][57][58] and have been routinely employed in the analysis of food. While the specified measured mass accuracies for these instruments are sufficient for non-targeted analysis, impaired data quality can occur, especially when analyzing complex sample matrices [58].…”

Section: Mass Spectramentioning

confidence: 99%

Non-targeted screening approaches for contaminants and adulterants in food using liquid chromatography hyphenated to high resolution mass spectrometry

Knolhoff

Croley

2016

Journal of Chromatography A

100

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“…Initial capabilities are limited to targeted search capabilities in preprocessed metabolomics data. Metabolomics platforms for which analysis tools are provided are LCMS [28,29], GCMS and GCGCMS. Preprocessed data can be acquired using the MetAlign software and stored in MADMAX.…”

Section: Metabolomics Analysismentioning

confidence: 99%

MADMAX – Management and analysis database for multiple ~omics experiments

Lin

Kools²,

Groot³

et al. 2011

Journal of Integrative Bioinformatics

Self Cite

120

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SummaryThe rapid increase of ~omics datasets generated by microarray, mass spectrometry and next generation sequencing technologies requires an integrated platform that can combine results from different ~omics datasets to provide novel insights in the understanding of biological systems. MADMAX is designed to provide a solution for storage and analysis of complex ~omics datasets. In addition, analysis results (such as lists of genes) can be merged to reveal candidate genes supported by all datasets. The system constitutes an ISA-Tab compliant LIMS part, which is linked to the different analysis pipelines. A pilot study of different type of ~omics data in Brassica rapa demonstrates the possible use of MADMAX. The web-based user interface provides easy access to data and analysis tools on top of the database. IntroductionTo better understand how phenotypes emerge, increasingly series of ~omics technologies (genomics, transcriptomics, proteomics, metabolomics) rather than individual measurements are necessarily used within a single study. Such efforts boost the demands of both data storage and data analysis of different high-throughput approaches. However, in the past it was hardly possible to store metadata from different ~omics technologies in the same repository. To accommodate this demand the ISA-Tab [1] format was proposed to build up a common structured representation of the metadata of studies from a combination of technologies. This also triggered attempts to develop data processing tools tailored to the needs of biologists. Unfortunately most of these tools have high demands on hardware requirements, or contain non-intuitive command line-based interfaces.* To whom correspondence should be addressed: jack.leunissen@wur.nl Here we present MADMAX, a multi-purpose database for the management and analysis of data from multiple ~omics experiments. It includes an ISA-Tab compliant backend database and a series of analysis pipelines for transcriptomics, metabolomics and genomics datasets; these pipelines are connected to the database through webservices such that other pipelines can be easily integrated into the current system ( Figure 1 Through the web interface, the user can store a complete experiment with all fields required in ISA-Tab format, sufficient to allow for subsequent analysis or even repeating the experiment later. Another section on the website is the central access to different analysis pipelines. Both individual analysis results and combined gene lists can be retrieved in the system for download. Centrally stored experiments and analysis results can only be accessed by the creator by default and will be accessible for other users only if the creator desires to share the data. The system is on an automatic backup schedule.MADMAX can be reached at http://madmax2.bioinformatics.nl/ and is available upon request by sending an email to madmax.request@bioinformatics.nl. ImplementationMADMAX is built upon an Oracle relational database on a Linux server and a computational analysis engine for different...

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Ultra-fast searching assists in evaluating sub-ppm mass accuracy enhancement in U-HPLC/Orbitrap MS data

Cited by 40 publications

References 11 publications

Structure Annotation and Quantification of Wheat Seed Oxidized Lipids by High-Resolution LC-MS/MS

Structure Annotation and Quantification of Wheat Seed Oxidized Lipids by High-Resolution LC-MS/MS

Non-targeted screening approaches for contaminants and adulterants in food using liquid chromatography hyphenated to high resolution mass spectrometry

MADMAX – Management and analysis database for multiple ~omics experiments

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