CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

Kuhl, Carsten; Tautenhahn, Ralf; Böttcher, Christoph; Larson, Tony R.; Neumann, Steffen

doi:10.1021/ac202450g

Cited by 981 publications

(898 citation statements)

References 26 publications

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“…LC-MS raw data in net.CDF format were processed using xcms (Smith et al, 2006) to pick and align peaks in the complete data set (Supplemental Protocol S1). CAMERA (Kuhl et al, 2012) was used to identify m/z features from the same analyte by deconvolution and to identify isotopes (Supplemental Protocol S1). Peaks eluting before 20 s or after 720 s were discarded.…”

Section: Raw Data Processingmentioning

confidence: 99%

“…Redundant MS/MS spectra (only the MS/MS spectrum with highest parent ion abundance in the MS scan was kept) and empty MS/MS spectra were removed. Within MS/MS spectra, all m/z values greater than the precursor ion, below 0.5% of the base peak intensity, lower than 100 counts, or isotopic and single charged (Kuhl et al, 2012) were removed. All remaining 8,957 nonredundant MS/MS spectra (Supplemental Fig.…”

Section: Raw Data Processingmentioning

confidence: 99%

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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: Raw Data Processingmentioning

confidence: 99%

Section: Raw Data Processingmentioning

confidence: 99%

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

2017

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“…Feature detection and retention time correction were done using XCMS (Smith et al 2006;Tautenhahn et al 2008). Peak list annotation was done in CAMERA (Kuhl et al 2012). All data features of interest were manually inspected for peak shape and alignment, and then mined against the Metlin database (Smith et al 2005) and the Human Metabolome Database (http://www.hmdb.ca/).…”

Section: Metabolomics Data Acquisition and Preprocessingmentioning

confidence: 99%

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

Abela

Simmons

Steindl

et al. 2015

J of Inher Metab Disea

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Clinical metabolomics has emerged as a powerful tool to study human metabolism in health and disease. Comparative statistical analysis of untargeted metabolic profiles can reveal perturbations of metabolite levels in diseases and thus has the potential to identify novel biomarkers. Here we have applied a simultaneous genetic-metabolomic approach in twin boys with epileptic encephalopathy of unclear etiology. Clinical exome sequencing identified a novel missense mutation in the spermine synthase gene (SMS) that causes Snyder-Robinson syndrome (SRS). Untargeted plasma metabolome analysis revealed significantly elevated levels of N(8)-acetylspermidine, a precursor derivative of spermine biosynthesis, as a potential novel plasma biomarker for SRS. This result was verified in a third patient with genetically confirmed SRS. This study illustrates the potential of metabolomics as a translational technique to support exome data on a functional and clinical level. Abstract Clinical metabolomics has emerged as a powerful tool to study human metabolism in health and disease. Comparative statistical analysis of untargeted metabolic profiles can reveal perturbations of metabolite levels in diseases and thus has the potential to identify novel biomarkers. Here we have applied a simultaneous genetic-metabolomic approach in twin boys with epileptic encephalopathy of unclear etiology. Clinical exome sequencing identified a novel missense mutation in the spermine synthase gene (SMS) that causes Snyder-Robinson syndrome (SRS). Untargeted plasma metabolome analysis revealed significantly elevated levels of N 8 -acetylspermidine, a precursor derivative of spermine biosynthesis, as a potential novel plasma biomarker for SRS. This result was verified in a third patient with genetically confirmed SRS. This study illustrates the potential of metabolomics as a translational technique to support exome data on a functional and clinical level.

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“…Missing peak data were filled in the peaklists generated from the ADB lowsusceptibility ash leaf samples compared with the peaklists generated from the ADB susceptible leaves. The resulting peaklists were annotated using the Bioconductor R package, CAMERA 109 . The peaks were grouped using 0.05% of the width of the full width at half maximum, and groups correlated using a P value of 0.05 and calculating correlation inside and across samples.…”

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confidence: 99%

Genome sequence and genetic diversity of European ash trees

Sollars

Harper

Kelly

et al. 2016

Nature

169

227

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Ash trees (genus. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we reanalyse association transcriptomic data 3 , yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.

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CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

Cited by 981 publications

References 26 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

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

Genome sequence and genetic diversity of European ash trees

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CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

Cited by 981 publications

References 26 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

N8‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics

Genome sequence and genetic diversity of European ash trees

Contact Info

Product

Resources

About

N⁸‐acetylspermidine as a potential plasma biomarker for Snyder‐Robinson syndrome identified by clinical metabolomics