Petroleomics: Chemistry of the underworld Marshall, Alan G; Rodgers, Ryan P
Proceedings of the National Academy of Sciences - PNAS,
11/2008, Letnik:
105, Številka:
47
Journal Article
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Each different molecular elemental composition--e.g., CcHhNnOoSs--has a different exact mass. With sufficiently high mass resolving power (m/Δm₅₀% almost equal to 400,000, in which m is molecular ...mass and Δm₅₀% is the mass spectral peak width at half-maximum peak height) and mass accuracy (<300 ppb) up to almost equal to800 Da, now routinely available from high-field (greater-than-or-equal9.4 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 (NnOoSs), 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.
Lysyl-tRNA synthetase (LysRS), a component of the translation apparatus, is released from the cytoplasmic multi-tRNA synthetase complex (MSC) to activate the transcription factor MITF in stimulated ...mast cells through undefined mechanisms. Here we show that Ser207 phosphorylation provokes a new conformer of LysRS that inactivates its translational function but activates its transcriptional function. The crystal structure of an MSC subcomplex established that LysRS is held in the MSC by binding to the N terminus of the scaffold protein p38/AIMP2. Phosphorylation-created steric clashes at the LysRS domain interface disrupt its binding grooves for p38/AIMP2, releasing LysRS and provoking its nuclear translocation. This alteration also exposes the C-terminal domain of LysRS to bind to MITF and triggers LysRS-directed production of the second messenger Ap4A that activates MITF. Thus our results establish that a single conformational change triggered by phosphorylation leads to multiple effects driving an exclusive switch of LysRS function from translation to transcription.
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► Phosphorylation of Ser207 triggers a structural opening of LysRS in mast cell ► The open conformer releases LysRS from the multi-tRNA-synthetase complex ► It traps tRNA in an inactive state and switches off the canonical function of LysRS ► It drives Ap4A production and LysRS-MITF interaction for gene transcription in cell
We describe the design and initial performance of the first 21 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The 21 tesla magnet is the highest field superconducting ...magnet ever used for FT-ICR and features high spatial homogeneity, high temporal stability, and negligible liquid helium consumption. The instrument includes a commercial dual linear quadrupole trap front end that features high sensitivity, precise control of trapped ion number, and collisional and electron transfer dissociation. A third linear quadrupole trap offers high ion capacity and ejection efficiency, and rf quadrupole ion injection optics deliver ions to a novel dynamically harmonized ICR cell. Mass resolving power of 150,000 (
m/Δm
50%
) is achieved for bovine serum albumin (66 kDa) for a 0.38 s detection period, and greater than 2,000,000 resolving power is achieved for a 12 s detection period. Externally calibrated broadband mass measurement accuracy is typically less than 150 ppb rms, with resolving power greater than 300,000 at
m/z
400 for a 0.76 s detection period. Combined analysis of electron transfer and collisional dissociation spectra results in 68% sequence coverage for carbonic anhydrase. The instrument is part of the NSF High-Field FT-ICR User Facility and is available free of charge to qualified users.
Graphical Abstract
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•IHSS Pony Lake and Suwannee River fulvic acid DOM reference samples compared.•Molecular constituents assigned and characterized using FT-ICR MS.•Complementary data obtained from fluorescence ...spectroscopy.•Proteinaceous signatures of Pony Lake DOM assigned from both analytical methods.•More reactive/microbial character for Pony Lake DOM than for Suwannee River DOM.
We present the extensive characterization of Antarctic Pony Lake (PL) dissolved organic matter (DOM), an International Humic Substance Society (IHSS) fulvic acid (FA) reference standard, using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) and excitation–emission matrix fluorescence spectroscopy (EEMS). PLFA is the first reference standard available through IHSS derived solely from a microbial source. A number of factors differentiate PLFA from other IHSS standards, including source material, geographic location, sunlight exposure, freeze–thaw conditions, and other in situ environmental influences. ESI FT-ICR MS and EEMS were used to compare the PLFA microbial DOM compositional signature with the IHSS Suwannee River (SR) FA, a standard frequently studied for environmental DOM analysis. Although CcHhOoNnSs (n=0, 1, or 2 and s=0 or 1) constituents were present in both IHSS samples, PLFA contained more N and S molecular species, whereas SRFA was dominated by CcHhOo compounds. Proteinaceous character was detected with both methods, in greater abundance for PLFA, which we attributed to its microbial source material and labile, potentially more reactive nature than SRFA. Characterization from both analytical techniques resulted in complementary data that reinforce the importance of PLFA as an IHSS reference standard that should be utilized for other microbiological environmental DOM comparisons.
Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry has recently revealed that petroleum crude oil contains heteroatom-containing (N,O,S) organic components having more ...than 20 000 distinct elemental compositions (C c H h N n O o S s ). It is therefore now possible to contemplate the ultimate characterization of all of the chemical constituents of petroleum, along with their interactions and reactivity, a concept we denote as “petroleomics”. Such knowledge has already proved capable of distinguishing petroleum and its distillates according to their geochemical origin and maturity, distillation cut, extraction method, catalytic processing, etc. The key features that have opened up this new field have been (a) ultrahigh-resolution FT-ICR mass analysis, specifically, the capability to resolve species differing in elemental composition by C3 vs SH4 (i.e., 0.0034 Da); (b) higher magnetic field to cover the whole mass range at once; (c) dynamic range extension by external mass filtering; and (d) plots of Kendrick mass defect vs nominal Kendrick mass as a means for sorting different compound “classes” (i.e., numbers of N, O, and S atoms), “types” (rings plus double bonds), and alkylation ((−CH2) n ) distributions, thereby extending to >900 Da the upper limit for unique assignment of elemental composition based on accurate mass measurement. The same methods are also being applied successfully to analysis of humic and fulvic acids, coals, and other complex natural mixtures, often without prior or on-line chromatographic separation.
Twenty-five years ago, Boduszynski et al. conducted a comprehensive study of heavy oil composition and concluded that crude oil composition increases gradually and continuously with regard to ...aromaticity, molecular weight, and heteroatom content from the light distillates to non-distillables (the Boduszynski continuum model). Previous exhaustive characterization of heavy vacuum gas oil by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provided compositional data that strongly supports the continuum model. However, when the molecular formulas obtained by FT-ICR MS for the distillates and asphaltenes from the same parent crude oil are plotted as double bond equivalents (DBE) versus carbon number, a gap appears between the compositional space of “asphaltenes” and “maltenes”, in contradiction to the Boduszynski–Altgelt model. Here, a heavy distillate cut (atmospheric equivalent boiling point of 523–593 °C) is fractionated according to the number of aromatic rings by HPLC-2. The C7-deasphalted whole oil (C7-DAO), its pentane soluble/insoluble fractions, and each of their ring number fractions are comprehensively characterized by atmospheric pressure photoionization (APPI) FT-ICR MS and tandem mass spectrometry (MS/MS). The HPLC-2 fractions from both the C5-soluble and C5-insoluble C7-DAO represent a gradual and continuous progression that fills the compositional “gap” in carbon number and aromaticity between asphaltenes and maltenes as a function of the increasing aromatic ring number, as predicted by Boduszynski. MS/MS results indicate that each ring number fraction comprises both island and archipelago structural motifs. FT-ICR MS reveals a continuum in carbon number and aromaticity. The C5-insoluble C7-DAO components have a similar structure but with higher-order fused ring core structures and are composed of a higher proportion of archipelago structures than the C5-soluble C7-DAO components. Thus, fractionation by the aromatic ring number of “maltenic” and “asphaltenic” species from the C7-solubles from a high boiling distillate validates the compositional continuum of petroleum components, and MS/MS exposes the aromatic building blocks of “maltenic” and “asphaltenic” species (structural continuum) that comprise island and archipelago structural motifs.
The detailed molecular composition of water-soluble atmospheric organic matter (AOM) contained in fog water was studied by use of electrospray ionization ultrahigh-resolution Fourier transform ion ...cyclotron resonance mass spectrometry. We identified 1368 individual molecular masses in the range of 100−400 Da from negative-ion spectra obtained after reversed-phase extraction with a hydrophilic solid phase sorbent. The detected organic anions are multifunctional with a variety of oxygenated functional groups. We observe organic nitrogen, organic sulfur, and organic nitrogen−sulfur compounds as well as many species with only C, H, and O elemental composition. Analysis of the double bond equivalents (DBE = the number of rings plus the number of double bonds to carbon) suggests that these compound structures range from highly aliphatic to aromatic with DBE values of 1−11. The compounds range in their extent of oxidation with oxygen to carbon ratios from 0.2 to 2 with an average value of 0.43. Several homologous series of compounds and multifunctional oligomers were identified in this AOM. The high extent of homologous series of compounds likely originates from primary components that have become oxidized. The multifunctional oligomers appear to represent atmospheric processing of primary and secondary compounds. The isolated water-soluble components identified here are amphiphilic, meaning that they contain both hydrophilic oxygenated functional groups and hydrophobic aliphatic and aromatic structural moieties. Despite the high number of compounds with very high oxygen content, 60% of assigned chemical formulas have measured organic mass-to-organic carbon ratios ≤2.25 (ranging from 1.25 to 3.5). Because the results reported here are not quantitative, an average ratio cannot be determined.
Vanadyl porphyrins are detected and characterized by their double-bond equivalents (DBE = number of rings plus double bonds) and carbon number in an unfractionated (raw) asphaltene and unaltered ...South American crude oil. Atmospheric pressure photoionization (APPI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides the high mass-resolving power (450 000−650 000 at m/z 500) and accurate mass (<300 ppb) to unambiguously assign elemental compositions to each of more than 10 000 peaks in each mass spectrum. Kendrick mass sorting revealed unusually high mass errors for peaks assigned to high DBE O2 species as well as a suspicious bimodal distribution in plots of DBE versus carbon number for all O2 species. Inclusion of vanadium in the chemical formula assignment resolved the bimodal distribution into lower DBE O2 species and vanadyl porphyrins, with a subsequent decrease in mass assignment errors to the same level as those for the thousands of other identified species. Vanadyl porphyrins are detected as both M+ • and M + H+ molecular and quasimolecular ions. Trends in the relative abundance of specific DBE values reveal the structural diversity of the vanadyl porphyrins in the asphaltene and heavy crude oil. To our knowledge, the current results are the first to directly identify and catalog the structural diversity of vanadyl porphyrins directly in raw (unfractionated) asphaltene and unaltered heavy crude oil.
Petroleum emulsion interfacial material (species that reside in the water/oil interface) are believed to be responsible for stabilizing emulsions in petroleum; therefore, their characterization can ...help to develop strategies to mitigate/manipulate petroleum emulsions. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has shown that the species present at the oil/water interface are enriched in sulfur- and oxygen-containing functionalities. However, structural and isomeric information about the chemical functionalities is still uncertain. Here, we demonstrate the potential of ion mobility mass spectrometry (IM-MS) combined with post-ion mobility collision-induced dissociation (post-IM CID) to characterize functional isomers in petroleum emulsion interfacial material. Interfacial material was isolated from Athabasca bitumen and a heavy crude oil by the wet silica method. IM time-of-flight (TOF) MS analysis shows the presence of multiple isomeric O3S1 species in both samples. Post-IM CID helps to identify the mobility-separated isomers; losses of CO2, H2O, and CO2 + H2O indicate the presence of a carboxylic group (naphthenic acids) and possibly a hydroxyl group, whereas losses of an alkyl chain to yield fragment ions with 4 double bond equivalents as well as the formation of SO3 • – suggest alkylbenzenesulfonates. Alkylbenzenesulfonates correspond to surfactants commonly added to petroleum, as confirmed by a comparison to a standard mixture of linear alkylbenzenesulfonates (LAS). The characterization and distinction of the isomers by CID is possible even in samples containing a mixture of functionalities by virtue of pre-separation by ion mobility. Emulsion interfacial material isolated from both Athabasca bitumen and heavy crude oil contains a mixture of functional isomers. Post-IM CID also allows for the use of diagnostic fragment ions to deconvolve incompletely resolved IM peaks. The deconvolution shows that synthetic surfactants (LAS) are more abundant in the emulsion interfacial material from the heavy crude oil, whereas naturally occurring SO3 naphthenic acids are predominant in Athabasca bitumen. FT-ICR mass spectral data confirm the IM-TOF molecular formula assignments and reveal that isobaric ions of different mobilities are indeed isomers.
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