Resolution and Chemical Formula Identification of Aromatic Hydrocarbons and Aromatic Compounds Containing Sulfur, Nitrogen, or Oxygen in Petroleum Distillates and Refinery Streams

Guan, Shenheng; Marshall, Alan G.; Scheppele, Stuart E.

doi:10.1021/ac9507855

Cited by 133 publications

(118 citation statements)

References 56 publications

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“…The described method involved the determination of peptide ion m/z values by FT-ICR SIM scans recorded over a narrow m/z range around the analyzed ions. The small m/z range allowed high peptide ion S/N values even when only a small number of ions were analyzed in the ICR cell (37). By using the AGC to ensure that a constantly low number of ions was subjected to SIM scans, space-charge effects were avoided, and an excellent mass accuracy was achieved.…”

Section: Optimization Of Mass Accuracy On the Ltq Ft Mass Spectrometer-mentioning

confidence: 99%

Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics

Haas

Faherty

Gerber

et al. 2006

Molecular & Cellular Proteomics

261

305

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Mass spectrometers that provide high mass accuracy such as FT-ICR instruments are increasingly used in proteomic studies. Although the importance of accurately determined molecular masses for the identification of biomolecules is generally accepted, its role in the analysis of shotgun proteomic data has not been thoroughly studied. To gain insight into this role, we used a hybrid linear quadrupole ion trap/FT-ICR (LTQ FT) mass spectrometer for LC-MS/MS analysis of a highly complex peptide mixture derived from a fraction of the yeast proteome. We applied three data-dependent MS/MS acquisition methods. The FT-ICR part of the hybrid mass spectrometer was either not exploited, used only for survey MS scans, or also used for acquiring selected ion monitoring scans to optimize mass accuracy. MS/MS data were assigned with the SEQUEST algorithm, and peptide identifications were validated by estimating the number of incorrect assignments using the composite target/decoy database search strategy. We developed a simple mass calibration strategy exploiting polydimethylcyclosiloxane background ions as calibrant ions. This strategy allowed us to substantially improve mass accuracy without reducing the number of MS/MS spectra acquired in an LC-MS/MS run. The benefits of high mass accuracy were greatest for assigning MS/MS spectra with low signal-to-noise ratios and for assigning phosphopeptides. Confident peptide identification rates from these data sets could be doubled by the use of mass accuracy information. It was also shown that improving mass accuracy at a cost to the MS/MS acquisition rate substantially lowered the sensitivity of LC-MS/MS analyses. The use of FT-ICR selected ion monitoring scans to maximize mass accuracy reduced the number of protein identifications by 40%. MS has become the method of choice for the characterization of complex protein mixtures from cells or tissues (1). The highest throughput and most comprehensive efforts to catalog protein mixtures have so far been achieved using a strategy known as shotgun proteomics (2). Proteins are proteolytically digested, and the resultant peptide mixture is usually separated by reversed-phase LC coupled on line to a mass spectrometer. Peptides are ionized and subjected to sequencing by MS/MS. Peptide ion sequences are derived based on fragment ions predominately formed through backbone cleavage at amide bonds. Several algorithms such as SEQUEST (3) and Mascot (4) allow automated assignment of MS/MS spectra by matching acquired data with spectra predicted on the basis of protein sequence databases (5). The protein composition of the analyzed sample is ultimately inferred from identified peptides (6).Recent MS technologies facilitate the acquisition of many thousands of MS/MS spectra over the course of one LC-MS/MS analysis. In general, only a portion of these spectra are correctly assigned to peptide ions using current database search algorithms. Low quality MS/MS data, non-peptide ions selected for fragmentation, and peptide ions where the corresponding sequenc...

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Section: Optimization Of Mass Accuracy On the Ltq Ft Mass Spectrometer-mentioning

confidence: 99%

Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics

Haas

Faherty

Gerber

et al. 2006

Molecular & Cellular Proteomics

261

305

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“…The metabolome data were composed of mass-to-charge ratio (m/z) values with ion intensities using an FT-ICR/MS metabolomics scheme (Oikawa et al 2006). Among a variety of MS principles, FT-ICR/MS offers the best performance in terms of the mass resolution as it allows for precise molecular formula prediction (Guan et al 1996;Marshall et al 1998), a key step for metabolite identification. Principal component analysis (PCA) demonstrated that the root metabolomes formed in the cyp81f4 lines clearly differed from those in wild-type plants ( Figure 4A), with the PC1 (59.2%) and PC2 (16.7%) separation shown in Supplementary Table 2.…”

Section: Metabolomics With Cyp81f4 T-dna Insertion Mutantsmentioning

confidence: 99%

Metabolomic characterization of the possible involvement of a Cytochrome P450, CYP81F4, in the biosynthesis of indolic glucosinolate in Arabidopsis

Kai

Takahashi

Saga

et al. 2011

Plant Biotechnology

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Plants produce and accumulate a wide variety of secondary metabolites. In such diverse secondary metabolisms, precursor structures are modified through biochemical steps driven by different enzyme classes. These enzyme classes are categorized according to their catalytic principles conferred by specific amino acid sequence motifs, and individual enzymes belonging to each class catalyze their reactions on the basis of the same catalytic principle but with different substrates. Such enzyme classes are ubiquitously found across kingdoms. For example, the Arabidopsis genome contains at least 24 flavin-containing monooxygenase genes, 272 cytochrome P450 genes, and more than 20 Sadenosylmethionine-dependent methyltransferase genes. Such tentative gene annotations should be confirmed in terms of actual biological functions.Metabolomics focuses on full biochemical events as an integral outcome of genome-wide gene expression and is thus expected to play a crucial role in gene annotation and curation pipelines (Fukushima et al. 2009; Schauer and Fernie 2006). Current metabolomics studies rely on the systematic comparison of detectable analytes with reference standard compounds on a variety of analytical platforms. These metabolomics studies have demonstrated their robustness in metabolic engineering, process engineering, biomarker finding, and the functional characterization of novel genes. It is of note, however, that reference standards are usually not available to clarify unknown compounds on the basis of analytical chemistry-based evidence. This is also the case for the functional characterization of recombinant enzymes acting on unidentified substrates. Thus, unique analytical methodologies independent of reference standards/substrates are necessary for the characterization of metabolic genes of unknown functions.In this study, we applied a pathway simulation method on van Krevelen diagrams using the metabolome information from an in-house metabolomics scheme based on Fourier transform ion cyclotron resonance mass Abstract We studied the biosynthetic role of a cytochrome P450, CYP81F4, in Arabidopsis. The CYP81F4 gene was found within a gene expression network containing the transcription factor gene MYB34/ATR1 involved in tryptophan metabolisms. Root metabolic profiles in null cyp81f4 mutant lines were analyzed using an in-house metabolomics scheme based on Fourier transform ion cyclotron resonance mass spectrometry. The cyp81f4 mutant plants exhibited a build-up of indole-3-yl-methyl glucosinolate with concomitant loss of 1-methoxy-indole-3-yl-methyl glucosinolate. A pathway prediction supported by a detailed glucosinolate analysis indicated that CYP81F4, together with an unidentified methyltransferase, is involved in the formation of the methoxy group in the indole ring to yield 1-methoxy-indole-3-ylmethyl glucosinolate in Arabidopsis roots. Current results suggest that 1-methoxy-indole-3-yl-methyl glucosinolate is produced by the activity of CYP81F4 in Arabidopsis roots.Key words: Cytochrome P450, gene coexpressi...

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“…It was first applied to petroleum via electron ionization of petroleum distillates (3,4). However, the relatively low magnetic field (3.0 T) limited the m/z range, the need to volatilize the sample limited the molecular weight range (especially for heteroatomcontaining species), and electron ionization produced extensive fragmentation (especially of alkyl chains).…”

mentioning

confidence: 99%

Petroleomics: Chemistry of the underworld

Marshall

Rodgers

2008

Proc. Natl. Acad. Sci. U.S.A.

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620

565

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Each different molecular elemental composition-e.g., CcHhNnOoSshas a different exact mass. With sufficiently high mass resolving power (m/⌬m 50% Ϸ 400,000, in which m is molecular mass and ⌬m50% is the mass spectral peak width at half-maximum peak height) and mass accuracy (<300 ppb) up to Ϸ800 Da, now routinely available from high-field (>9.4 T) Fourier transform ion cyclotron resonance mass spectrometry, it is possible to resolve and identify uniquely and simultaneously each of the thousands of elemental compositions from the most complex natural organic mixtures, including petroleum crude oil. It is thus possible to separate and sort petroleum components according to their heteroatom class (N nOoSs), double bond equivalents (DBE ‫؍‬ number of rings plus double bonds involving carbon, because each ring or double bond results in a loss of two hydrogen atoms), and carbon number. ''Petroleomics'' is the characterization of petroleum at the molecular level. From sufficiently complete characterization of the organic composition of petroleum and its products, it should be possible to correlate (and ultimately predict) their properties and behavior. Examples include molecular mass distribution, distillation profile, characterization of specific fractions without prior extraction or wet chemical separation from the original bulk material, biodegradation, maturity, water solubility (and oil:water emulsion behavior), deposits in oil wells and refineries, efficiency and specificity of catalytic hydroprocessing, ''heavy ends'' (asphaltenes) analysis, corrosion, etc.Fourier transform ͉ ion cyclotron resonance ͉ mass spectrometry ͉ petroleum ͉ fossil fuel

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Resolution and Chemical Formula Identification of Aromatic Hydrocarbons and Aromatic Compounds Containing Sulfur, Nitrogen, or Oxygen in Petroleum Distillates and Refinery Streams

Cited by 133 publications

References 56 publications

Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics

Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics

Metabolomic characterization of the possible involvement of a Cytochrome P450, CYP81F4, in the biosynthesis of indolic glucosinolate in Arabidopsis

Petroleomics: Chemistry of the underworld

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