Single Mass Spectrum Research Articles

Quality Control Based on Isotopic Distributions for High-Throughput MALDI-TOF and MALDI-FTICR Serum Peptide Profiling

In this study, we have implemented a new quality control (QC) parameter for peptide profiling based on isotopic distributions. This QC parameter is an objective measure and facilitates automatic sorting of large numbers of peptide spectra. Peptides in human serum samples were enriched using reversed-phase C(18)-functionalized magnetic beads using a high-throughput robotic platform. High-resolution MALDI-TOF and ultrahigh resolution MALDI-FTICR mass spectra were obtained and a workflow was developed for automated analysis and evaluation of these profiles. To this end, the isotopic distributions of multiple peptides were quantified from both MALDI-TOF and MALDI-FTICR spectra. Odd peptide isotope distributions in TOF spectra could be rationalized from ultrahigh resolution FTICR spectra that showed overlap of different peptides. The comparison of isotope patterns with estimated polyaveragine distributions was used to calculate a QC value for each single mass spectrum. Sorting these QC values enabled the best MALDI spectrum to be selected from replicate spots. Moreover, using this approach spectra containing high intensities of polymers or other contaminants and lacking peptides of interest can be efficiently removed from a clinical dataset. In general, this method simplifies the exclusion of low quality spectra from further statistical analysis.

Petroleomics: A Test Bed for Ultra-High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Within a relative abundance dynamic range of approximately 10,000:1, the world's most compositionally complex organic mixture is petroleum crude oil. As such, it provides the most challenging target for mass spectral resolution and identification of molecules below m/z 2000. The mass "splits" in petroleum include most of those that also appear in proteomics, metabolomics and other complex organic mixture analysis. Therefore, petroleum provides an excellent test bed for optimizing mass spectrometer performance in general. The presence of multiple elemental compositions spanning less than 1 Da in mass facilitates mapping and correction of rf phase variation across a Fourier transform ion cyclotron resonance mass spectrum, as well as exposing otherwise inaccessible systematic mass deviations, for additional improvement in mass resolving power and mass accuracy by a factor of up to 5. Internal mass calibration, combined with systematic peak assignment for successive homologous series, enables automated elemental composition assignment of tens of thousands of peaks in a single mass spectrum.

Comparison of FTIR and Particle Mass Spectrometry for the Measurement of Particulate Organic Nitrates

While multifunctional organic nitrates are formed during the atmospheric oxidation of volatile organic compounds, relatively little is known about their signatures in particle mass spectrometers. High resolution time-of-flight aerosol mass spectrometry (HR-ToF-AMS) and FTIR spectroscopy on particles impacted on ZnSe windows were applied to NH(4)NO(3), NaNO(3), and isosorbide 5-mononitrate (IMN) particles, and to secondary organic aerosol (SOA) from NO(3) radical reactions at 22 degrees C and 1 atm in air with alpha- and beta-pinene, 3-carene, limonene, and isoprene. For comparison, single particle laser ablation mass spectra (SPLAT II) were also obtained for IMN and SOA from the alpha-pinene reaction. The mass spectra of all particles exhibit significant intensity at m/z 30, and for the SOA, weak peaks corresponding to various organic fragments containing nitrogen [C(x)H(y)N(z)O(a)](+) were identified using HR-ToF-AMS. The NO(+)/NO(2)(+) ratios from HR-ToF-AMS were 10-15 for IMN and the SOA from the alpha- and beta-pinene, 3-carene, and limonene reactions, approximately 5 for the isoprene reaction, 2.4 for NH(4)NO(3) and 80 for NaNO(3). The N/H ratios from HR-ToF-AMS for the SOA were smaller by a factor of 2 to 4 than the -ONO(2)/C-H ratios measured using FTIR. FTIR has the advantage that it provides identification and quantification of functional groups. The NO(+)/NO(2)(+) ratio from HR-ToF-AMS can indicate organic nitrates if they are present at more than 15-60% of the inorganic nitrate, depending on whether the latter is NH(4)NO(3) or NaNO(3). However, unique identification of specific organic nitrates is not possible with either method.

Electron‐capture dissociation (ECD), collision‐induced dissociation (CID) and ECD/CID in a linear radio‐frequency‐free magnetic cell

Electron‐capture dissociation (ECD), collision‐induced dissociation (CID) and ECD/CID in a linear radio‐frequency‐free magnetic cell

Structural characterization of a poly(methacrylic acid)–poly(methyl methacrylate) copolymer by nuclear magnetic resonance and mass spectrometry

Mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been combined to achieve the complete microstructural characterization of a poly(methacrylic acid)–poly(methyl methacrylate) (PMAA–PMMA) copolymer synthesized by nitroxide-mediated polymerization. Various PMAA–PMMA species could be identified which mainly differ in terms of terminaisons. 1H and 13C NMR experiments revealed the structure of the end-groups as well as the proportion of each co-monomer in the copolymers. These end-group masses were further confirmed from m/ z values of doubly charged copolymer anions detected in the single stage mass spectrum. In contrast, copolymer composition derived from MS data was not consistent with NMR results, obviously due to strong mass bias well known to occur during electrospray ionization of these polymeric species. Tandem mass spectrometry could reveal the random nature of the copolymer based on typical dissociation reactions, i.e., water elimination occurred from any two contiguous MAA units while MAA–MMA pairs gave rise to the loss of a methanol molecule. Polymer backbone cleavages were also observed to occur and gave low abundance fragment ions which allowed the structure of the initiating end-group to be confirmed.

On Performing Simultaneous Electron Transfer Dissociation and Collision-Induced Dissociation on Multiply Protonated Peptides in a Linear Ion Trap

We propose a tandem mass spectrometry method that combines electron-transfer dissociation (ETD) with simultaneous collision-induced dissociation (CID), termed ETD/CID. This technique can provide more complete sequence coverage of peptide ions, especially those at lower charge states. A selected precursor ion is isolated and subjected to ETD. At the same time, a residual precursor ion is subjected to activation via CID. The specific residual precursor ion selected for activation will depend upon the charge state and m/z of the ETD precursor ion. Residual precursor ions, which include unreacted precursor ions and charge-reduced precursor ions (either by electron-transfer or proton transfer), are often abundant remainders in ETD-only reactions. Preliminary results demonstrate that during an ETD/CID experiment, b, y, c, and z-type ions can be produced in a single experiment and displayed in a single mass spectrum. While some peptides, especially doubly protonated ones, do not fragment well by ETD, ETD/CID alleviates this problem by acting in at least one of three ways: (1) the number of ETD fragment ions are enhanced by CID of residual precursor ions, (2) both ETD and CID-derived fragments are produced, or (3) predominantly CID-derived fragments are produced with little or no improvement in ETD-derived fragment ions. Two interesting scenarios are presented that display the flexibility of the ETD/CID method. For example, smaller peptides that show little response to ETD are fragmented preferentially by CID during the ETD/CID experiment. Conversely, larger peptides with higher charge states are fragmented primarily via ETD. Hence, ETD/CID appears to rely upon the fundamental reactivity of the analyte cations to provide the best fragmentation without implementing any additional logic or MS/MS experiments. In addition to the ETD/CID experiments, we describe a novel dual source interface for providing front-end ETD capabilities on a linear ion trap mass spectrometer.

Mass spectra of methyl acetate and ethyl formate

We experimentally investigate the ionization and dissociation of two isomers, methyl acetate (CH 3COOCH 3) and ethyl formate (CH 3CH 2COOH), irradiated by strong laser pulses with a pulse duration of 7 fs. Strong parent ions are observed for both isomers. However, main fragmental ions are CH 3CO + and CH 3 + for methyl acetate and CH 3O + and C 2 H 4 + for ethyl formate. Through comparing with the single photon ionization mass spectra of these two isomers, we find that these fragments are produced by the direct dissociation of the parent ions in different excited electronic states.

FT-ICR MS optimization for the analysis of intact proteins

Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) remains the technique of choice for the analysis of intact proteins from complex biological systems, i.e., top-down proteomics. Recently, we have implemented a compensated open cylindrical ion trapping cell into a 12 T FT-ICR mass spectrometer. This new cell has previously demonstrated improved sensitivity, dynamic range, and mass measurement accuracy for the analysis of relatively small tryptic peptides. These improvements are due to the modified trapping potential of the cell which closely approximates the ideal harmonic trapping potential. Here, we report the instrument optimization for the analysis of large macro-molecular ions, such as proteins. Single transient mass spectra of multiply charged bovine ubiquitin ions with sub-ppm mass measurement accuracy, improved signal intensity, and increased dynamic range were obtained using this new cell with increased post-excitation cyclotron radii. The increased cyclotron radii correspond to increased ion kinetic energy and collisions between neutrals and ions with sufficient kinetic energy can exceed a threshold of single collision ion fragmentation. A transition then occurs from relatively long signal lifetimes at low excitation radii to potentially shorter lifetimes, defined by the average ion-neutral collision time. The proposed high energy ion loss mechanism is evaluated and compared with experimental results for bovine ubiquitin and serum albumin. We find that the analysis of large macro-molecules can be significantly improved by the further reduction of pressure in the ion trapping cell. This reduces the high energy ion losses and can enable increased sensitivity and mass measurement accuracy to be realized without compromising resolution. Further, these results appear to be generally applicable to FTMS, and it is expected that the high energy ion loss mechanism also applies to Orbitrap mass analyzers.

P.451 VEGF in the TMJ related to the clinical outcome

Secondary organic aerosol (SOA) formed from Cl-initiated oxidation of toluene was investigated in a home-made smog chamber. The size distribution and chemical composition of SOA particles were measured using aerodynamic particle sizer spectrometer and the aerosol laser time-of-flight mass spectrometer (ALTOFMS), respectively. According to a large number of single aerosol diameter and mass spectra, the size distribution and chemical composition of SOA were obtained statistically. Experimental results showed that SOA particles created by Cl-initiated oxidation of toluene is predominantly in the form of fine particles, which have diameters less than 2.5 μm (i.e., PM2.5), and glyoxal, benzaldehyde, benzyl alcohol, benzoquinone, benzoic acid, benzyl hydroperoxide and benzyl methyl nitrate are the major products components in the SOA. The possible reaction mechanisms leading to these products are also proposed.

In situ determination of atmospheric aerosol composition as a function of hygroscopic growth

An in situ measurement setup to determine the chemical composition of aerosols as a function of hygroscopicity is presented. This has been done by connecting a custom‐built Hygroscopicity Tandem Differential Mobility Analyzer (HTDMA) and an Aerosol Time‐of‐Flight Mass Spectrometer (ATOFMS), commercially available from TSI (Model 3800). Single particle bipolar mass spectra from aerosols leaving the HTDMA could thus be obtained as a function of the hygroscopic growth factor. For these studies the HTDMA was set at a relative humidity of 82% and particles with a dry diameter of 260 nm were selected. The setup was first laboratory tested, after which field experiments were performed. Two data sets were obtained during wintertime 2007 in Switzerland: the first in the urban Zurich environment and the other at the remote high alpine research station Jungfraujoch (JFJ). In Zurich, several thousand mass spectra were obtained in less than 2 days of sampling due to a high aerosol loading. At the JFJ, due to low particle concentrations in free tropospheric air masses, a longer sampling period was required. Both in Zurich and at the JFJ, two different growth factor modes were observed. Results from these two locations show that most aerosol particles were a mixture of several compounds. A large contribution of organics and combustion species was found in the less hygroscopic growth mode for both locations. Noncombustion refractory material (e.g., metals, mineral dust, and fly ash) was also highly enhanced in the nonhygroscopic particles. Sulfate, normally considered highly soluble, was found to be a constituent in almost all particles independent of their hygroscopic growth factor.

Targeted Online Liquid Chromatography Electron Capture Dissociation Mass Spectrometry for the Localization of Sites of in Vivo Phosphorylation in Human Sprouty2

We demonstrate a strategy employing collision-induced dissociation for phosphopeptide discovery, followed by targeted electron capture dissociation (ECD) for site localization. The high mass accuracy and low background noise of the ECD mass spectra allow facile sequencing of coeluting isobaric phosphopeptides, with up to two isobaric phosphopeptides sequenced from a single mass spectrum. In contrast to the previously described neutral loss dependent ECD method, targeted ECD allows analysis of both phosphotyrosine peptides and lower abundance phosphopeptides. The approach was applied to phosphorylation analysis of human Sprouty2, a regulator of receptor tyrosine kinase signaling. Fifteen sites of phosphorylation were identified, 11 of which are novel.

Increasing information from shotgun proteomic data by accounting for misassigned precursor ion masses

Although mass spectrometers are capable of providing high mass accuracy data, assignment of true monoisotopic precursor ion mass is complicated during data-dependent ion selection for LC-MS/MS analysis of complex mixtures. The complication arises when chromatographic peak widths for a given analyte exceed the time required to acquire a precursor ion mass spectrum. The result is that many measured monoisotopic masses are misassigned due to calculation from a single mass spectrum with poor ion statistics based on only a fraction of the total available ions for a given analyte. Such data in turn produces errors in automated database searches, where precursor m/z value is one search parameter. We propose here a postacquisition approach to correct misassigned monoisotopic m/z values that involves peak detection over the entire elution profile and correction of the precursor ion monoisotopic mass. As a result of using this approach to reprocess shotgun proteomic data we increased peptide sequence assignments by 10% while reducing the estimated false positive ratio from 1 to 0.2%. We also show that 4% of the salvaged identifications may be accounted for by correction of mixed tandem mass spectra resulting from fragmentation of multiple peptides simultaneously, a situation which we refer to as accidental CID.

Wavelength and size dependence in single particle laser aerosol mass spectra

The impact of particle size and desorption/ionization laser wavelength on ion signal in single particle laser mass spectrometry was investigated. Individual particles of α -cyano hydroxy-cinnamic acid, dihydroxy benzoic acid, and nitroguanadine were sized, tracked, and desorbed/ionized by 266 or 355 nm laser light, and the resulting mass spectra were analyzed. Sodium ion signal and total ion signal were determined. Sodium ion is a measure of desorption efficiency, while total ion signal is sensitive to both desorption and ionization. The sodium ion signal was found to be independent of wavelength, above a minimum laser energy which varied by compound. The total ion signal was found to be higher for 266 nm desorption/ionization laser mass spectra in most cases. The sodium ion and total ion signals were found to be linear with particle size, regardless of laser energy or wavelength. Both sodium ion and total ion signals were also found to vary roughly linearly with laser energy, showing a much weaker dependance on laser energy than predicted by MALDI results. These results suggest that the absorbance spectrum of the compound does not predict desorption and ionization efficiency, above some minimum laser energy.

Low‐Molecular Weight and Oligomeric Components in Secondary Organic Aerosol from the Photooxidation of p‐Xylene

AbstractA laboratory study was performed to investigate the composition of secondary organic aerosol (SOA) products from photooxidation of the aromatic hydrocarbon p‐xylene. The experiments were conducted by irradiating p‐xylene/CH3ONO/NO/air mixtures in a home‐made smog chamber. The aerosol time‐of‐flight mass spectrometer (ATOFMS) was used to measure the size and the chemical composition of individual secondary organic aerosol particles in real‐time. According to a large number of single aerosol diameters and mass spectra, the size distribution and chemical composition of SOA were determined statistically. Experimental results showed that aerosol created by p‐xylene photooxidation is predominantly in the form of fine particles, which have diameters less than 2.5 μm (i.e. PM2.5), and aromatic aldehyde, unsaturated dicarbonys, hydroxyl dicarbonys, and organic acid are major product components in the SOA after 2 hours photooxidation. After aging for more than 8 hours, about 10% of the particle mass consists of oligomers with a molecular mass up to 600 daltons. The possible reaction mechanisms leading to these products are also proposed.

A Model-Based Method for the Prediction of the Isotopic Distribution of Peptides

The process of monoisotopic mass determination, i.e., nomination of the correct peak of an isotopically resolved group of peptide peaks as a monoisotopic peak, requires prior information about the isotopic distribution of the peptide. This points immediately to the difficulty of monoisotopic mass determination, whereas a single mass spectrum does not contain information about the atomic composition of a peptide and therefore the isotopic distribution of the peptide remains unknown. To solve this problem a technique is required, which is able to estimate the isotopic distribution given the information of a single mass spectrum. Senko et al. calculated the average isotopic distribution for any mass peptide via the multinomial expansion (Yergey 1983), using a scaled version of the average amino acid Averagine (Senko et al. 1995). Another method, introduced by Breen et al., approximates the result of the multinomial expansion by a Poisson model (Breen et al. 2000). Although both methods perform well, they have their specific limitations. In this manuscript, we propose an alternative method for the prediction of the isotopic distribution based on a model for consecutive ratios of peaks from the isotopic distribution, similar in spirit to the approach introduced by Gay et al. (1999). The presented method is computationally simple and accurate in predicting the expected isotopic distribution. Further, we extend our method to estimate the isotopic distribution of sulphur-containing peptides. This is important because the naturally occurring isotopes of sulphur have an impact on the isotopic distribution of a peptide.

Atmospheric Pressure Photoionization Proton Transfer for Complex Organic Mixtures Investigated by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

To further clarify the role of dopant solvent in proton transfer in atmospheric pressure photoionization (APPI), we employ ultrahigh-resolution FT-ICR mass analysis to identify M(+*), [M + H](+), [M - H](-), and [M + D](+) species in toluene or perdeuterotoluene for an equimolar mixture of five pyrrolic and pyridinic nitrogen heterocyclic model compounds, as well as for a complex organic mixture (Canadian Athabasca bitumen middle distillate). In the petroleum sample, the protons in the [M + H](+) species originate primarily from other components of the mixture itself, rather than from the toluene dopant. In contrast to electrospray ionization, in which basic (e.g., pyridinic) species protonate to form [M + H](+) positive ions and acidic (e.g., pyrrolic) species deprotonate to form [M - H](-) negative ions, APPI generates ions from both basic and acidic species in a single positive-ion mass spectrum. Ultrahigh-resolution mass analysis (in this work, m/Deltam(50%) = 500,000, in which Deltam(50%) is the mass spectral peak full width at half-maximum peak height) is needed to distinguish various close mass doublets: (13)C versus (12)CH (4.5 mDa), (13)CH versus (12)CD (2.9 mDa), and H(2) versus D (1.5 mDa).

On the Proper Use of Mass Accuracy in Proteomics

Mass measurement is the main outcome of mass spectrometry-based proteomics yet the potential of recent advances in accurate mass measurements remains largely unexploited. There is not even a clear definition of mass accuracy in the proteomics literature, and we identify at least three uses of this term: anecdotal mass accuracy, statistical mass accuracy, and the maximum mass deviation (MMD) allowed in a database search. We suggest using the second of these terms as the generic one. To make the best use of the mass precision offered by modern instruments we propose a series of simple steps involving recalibration of the data on "internal standards" contained in every proteomics data set. Each data set should be accompanied by a plot of mass errors from which the appropriate MMD can be chosen. More advanced uses of high mass accuracy include an MMD that depends on the signal abundance of each peptide. Adapting search engines to high mass accuracy in the MS/MS data is also a high priority. Proper use of high mass accuracy data can make MS-based proteomics one of the most "digital" and accurate post-genomics disciplines.

To improve the quantification sensitivity of large molecular weight compounds – with ginsenosides as example

High cone voltage was used to improve the quantification sensitivity of large molecular weight compounds in high-performance liquid chromatography electrospray ionization mass spectrometry (HPLC/ESI-MS), with ginsenosides as example. Investigations on the effect of cone voltage showed that within a voltage range of 30-130 V, for all the ginsenosides tested, i.e., Rb(1), Rb(2), Rc, Rd, Re, R(f) and R(g1), an increase in the applied cone voltage can significantly increase the sensitivity of the method. The maximum sensitivity in the determination decreases with the decreasing molecular weight of the ginsenosides in the order of Rb(1) > Rb(2) > Rc > Re > Rd > R(g1) > R(f). At the high cone voltage of 130 V, both molecular weight and structural information was obtained from a single mass spectrum. It can also be used for isomer differentiation and determination of O-glycosidic linkages in ginsenosides. Linear relationships between the peak area response and concentration were observed in the range of 50-2 x 10(5) ng/mL, with the correlation coefficients >0.99. The limits of detection reached down to pg for ginsenosides. The method was successfully applied to the determination of ginsenosides in commercial ginseng samples.

Detection and identification of arginine modifications on methylglyoxal‐modified ribonuclease by mass spectrometric analysis

Analysis of the broad range of trace chemical modifications of proteins in biological samples is a significant challenge for modern mass spectrometry. Modification at lysine and arginine residues, in particular, causes resistance to digestion by trypsin, producing large tryptic peptides that are not readily sequenced by mass spectrometry. In this work, we describe the analysis of ribonuclease (RNase) modified by methylglyoxal (MGO) under physiological conditions. For detection of modifications, we use comparative analysis of the single combined spectra extracted from the full-scan MS data of the tryptic digests from native and modified proteins. This approach revealed 11 ions unique to MGO-modified RNase, including a 32-amino acid peptide containing a modified Arg-85 residue. Sequential digestion of MGO-modified RNase by endoproteinase Glu-C and trypsin was required to obtain peptides that were amenable to sequencing analysis. Arg-39 was identified as the main site of modification (35% modification) on MGO-modified Rnase, and the dihydroxyimidazolidine and hydroimidazolone derivatives were the main adducts formed, with minor amounts of the tetrahydropyrimidine and argpyrimidine derivatives. For identification of these products, we used variations in source voltage and collision energy to obtain the dehydration and decarboxylation products of the tetrahydropyrimidine-containing peptides and dehydration of the dihydroxyimidazoline-containing peptides. The resultant spectra were dependent on the cone voltage and collision energy, and analysis of spectra at various settings permitted structural assignments. These studies illustrate the usefulness of single combined mass spectra extracted from full-scan data and variations in source and collision cell voltages for detection and structural characterization of chemical adducts on proteins.

Chemical Composition and Reaction Mechanisms for Secondary Organic Aerosol from Photooxidation of Toluene

AbstractA laboratory study was carried out to investigate the secondary organic aerosol (SOA) products from photooxidation of the aromatic hydrocarbon toluene. The experiments were conducted by irradiating toluene/CH3ONO/NO/air mixtures in a home‐made smog chamber. The aerosol time‐of‐flight mass spectrometer (ATOFMS) was used to measure the size and the chemical composition of individual secondary organic aerosol particles in real‐time. According to a large number of single aerosol diameters and mass spectra, we obtained the size distribution and chemical composition of SOA statistically. Expeperimental results showed that aerosol created by toluene photooxidation is predominantly in the form of fine particles, which have diameters less than 2.5 μm (i.e. PM2.5), and the predominant components of aerosol are furane, methyl glyoxylic acid, phenol, benzaldehyde, benzyl alcohol, cresol, 3‐hydroxy‐2,4‐dioxo‐pentanal, methyl nitrophenol, and 5‐hydroxy‐4,6‐dioxo‐2‐heptenal. The possible reaction mechanisms leading to these products were also discussed.