High Mass Measurement Accuracy Research Articles

Development of a nanoLC LTQ Orbitrap Mass Spectrometric Method for Profiling Glycans Derived from Plasma from Healthy, Benign Tumor Control, and Epithelial Ovarian Cancer Patients

We report the development of split-less nano-flow liquid chromatography mass spectrometric analysis of glycans chemically cleaved from glycoproteins in plasma. Porous graphitized carbon operating under reverse-phase conditions and an amide-based stationary phase operating under hydrophilic interaction conditions are quantitatively compared for glycan separation. Both stationary phases demonstrated similar column efficiencies and excellent retention time reproducibility without an internal standard to correct for retention time shift. The 95% confidence intervals of the mean retention times were +/-4 s across 5 days of analysis for both stationary phases; however, the amide stationary phase was observed to be more robust. The high mass measurement accuracy of less than 2 ppm and fragmentation spectra provided highly confident identifications along with structural information. In addition, data are compared among samples derived from 10 healthy controls, 10 controls with a differential diagnosis of benign gynecologic tumors, and 10 diseased epithelial ovarian cancer patients (EOC). Two fucosylated glycans were found to be up-regulated in healthy controls and provided an accurate diagnostic value with an area under the receiver operator characteristic curve of 0.87. However, these same glycans provided a significantly less diagnostic value when used to differentiate EOC from benign tumor control samples with an area under the curve of 0.73.

Accurate mass analysis of N‐acyl‐homoserine‐lactones and cognate lactone‐opened compounds in bacterial isolates of Pseudomonas aeruginosa PAO1 by LC‐ESI‐LTQ‐FTICR‐MS

N-acyl-homoserine-lactones (AHSLs) are widely conserved signal molecules present in quorum sensing systems of Gram-negative bacteria such as Pseudomonas aeruginosa. We present here the results obtained with a hybrid linear trap/Fourier transform ion cyclotron resonance (LTQ-FTICR) mass spectrometer used to investigate the occurrence of AHSLs and cognate N-acyl-homoserines (AHSs) in bacterial isolates of P. aeruginosa (strain PAO1). Two hydrolysed AHSs were found in significant amounts, most likely formed through the lactone opening of N-3-oxo-decanoyl-L-homoserine-lactone (3OC10-HSL) and N-3-oxo-dodecanoyl-L-homoserine-lactone (3OC12-HSL). Structure elucidation of these ring-opened molecules, i.e. N-3-oxo-decanoyl-L-homoserine (3OC10-HS), and N-3-oxo-dodecanoyl-L-homoserine (3OC12-HS), which are not detected by bacterial biosensors, was performed by high-resolution and accurate mass measurements upon liquid chromatography (LC) and confirmed by tandem MS in the LTQ analyser. Assignment of chemical formula, with mass spectra in the form of [M+H]+, was significantly expedited by extracted ion chromatograms (XICs) because the number of potentially plausible formulae for each protonated signalling molecule was considerably reduced a priori by the LC behaviour, the high mass measurement accuracy available in FTICR mass spectra and the isotopic patterns. At least two concentration levels were observed in spent culture supernatants of P. aeruginosa: compounds at a relatively high content (5-15 microM) that is C4-HSL, 3OC10-HS, and 3OC12-HS and those occurring at a lower content (<0.2 microM) that is C6-HSL and C8-HSL. The implications of this work extend to a great variety of Gram-negative bacteria.

Mechanism of [M + H] + Formation in Atmospheric Pressure Photoionization Mass Spectrometry: Identification of Propionitrile in Acetonitrile with High Mass Accuracy Measurement and Tandem Mass Spectrometry and Evidence for Its Involvement in the Protonation Phenomenon

The role of propionitrile in the production of [M+H]+ under atmospheric pressure photoionization (APPI) was investigated. In dopant-assisted APPI using acetone and anisole, protonated acetone and anisole radical cations were the most prominent ions observed. In dopant-free or direct APPI in acetonitrile, however, a major ion in acetonitrile was detected and identified as propionitrile, using high accuracy mass measurement and collision induced dissociation studies. Vaporizing ca. 10(-5) M althiazide and bendroflumethazide under direct APPI in acetonitrile produced their corresponding protonated species [M+H]+. In addition to protonated acetonitrile, its dimers, and acetonitrile/water clusters, protonated propionitrile, propionitrile dimer, and propionitrile/water clusters were also observed. The role of propionitrile, an impurity in acetonitrile and/or a possible product of ion-molecule reaction, in the production of [M+H]+ of althiazide and bendroflumethazide was further investigated in the absence of dopant using propionitrile-d5. The formation of [M+D]+ species was observed, suggesting a possible role of propionitrile in the protonation process. Additionally, an increase in the [M+H]+ signal of althiazide and bendroflumethazide was observed as a function of propionitrile concentration in acetonitrile. Theoretical data from the literature supported the assumption that one possible mechanism, among others, for the formation of [M+H]+ could be attributed to photo-initiated isomerization of propionitrile. The most stable isomers of propionitrile, based on their calculated ionization energy (IE) and relative energy (DeltaE), were assumed to undergo proton transfer to the analytes, and mechanisms were proposed.

MLLTRAP: A Penning trap facility for high-accuracy mass measurements

The MLLTRAP, presently under construction at the Maier-Leibnitz-Laboratory (Garching), is a Penning trap facility designed to combine several novel techniques to decelerate, purify, charge breed and cool the reaction products and perform high-accuracy nuclear mass measurements of highly charged, laser-cooled ions.

High-performance liquid chromatography–tandem mass spectrometry in the identification and determination of phase I and phase II drug metabolites

Applications of tandem mass spectrometry (MS/MS) techniques coupled with high-performance liquid chromatography (HPLC) in the identification and determination of phase I and phase II drug metabolites are reviewed with an emphasis on recent papers published predominantly within the last 6 years (2002–2007) reporting the employment of atmospheric pressure ionization techniques as the most promising approach for a sensitive detection, positive identification and quantitation of metabolites in complex biological matrices. This review is devoted to in vitro and in vivo drug biotransformation in humans and animals. The first step preceding an HPLC-MS bioanalysis consists in the choice of suitable sample preparation procedures (biomatrix sampling, homogenization, internal standard addition, deproteination, centrifugation, extraction). The subsequent step is the right optimization of chromatographic conditions providing the required separation selectivity, analysis time and also good compatibility with the MS detection. This is usually not accessible without the employment of the parent drug and synthesized or isolated chemical standards of expected phase I and sometimes also phase II metabolites. The incorporation of additional detectors (photodiode-array UV, fluorescence, polarimetric and others) between the HPLC and MS instruments can result in valuable analytical information supplementing MS results. The relation among the structural changes caused by metabolic reactions and corresponding shifts in the retention behavior in reversed-phase systems is discussed as supporting information for identification of the metabolite. The first and basic step in the interpretation of mass spectra is always the molecular weight (MW) determination based on the presence of protonated molecules [M+H]+ and sometimes adducts with ammonium or alkali-metal ions, observed in the positive-ion full-scan mass spectra. The MW determination can be confirmed by the [M-H]- ion for metabolites providing a signal in negative-ion mass spectra. MS/MS is a worthy tool for further structural characterization because of the occurrence of characteristic fragment ions, either MSn analysis for studying the fragmentation patterns using trap-based analyzers or high mass accuracy measurements for elemental composition determination using time of flight based or Fourier transform mass analyzers. The correlation between typical functional groups found in phase I and phase II drug metabolites and corresponding neutral losses is generalized and illustrated for selected examples. The choice of a suitable ionization technique and polarity mode in relation to the metabolite structure is discussed as well.

DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

DeconMSn accurately determines the monoisotopic mass and charge state of parent ions from high-resolution tandem mass spectrometry data, offering significant improvement for LTQ_FT and LTQ_Orbitrap instruments over the commercially delivered Thermo Fisher Scientific's extract_msn tool. Optimal parent ion mass tolerance values can be determined using accurate mass information, thus improving peptide identifications for high-mass measurement accuracy experiments. For low-resolution data from LCQ and LTQ instruments, DeconMSn incorporates a support-vector-machine-based charge detection algorithm that identifies the most likely charge of a parent species through peak characteristics of its fragmentation pattern. http://ncrr.pnl.gov/software/ or http://www.proteomicsresource.org/.

Towards a magnetic field stabilization at ISOLTRAP for high-accuracy mass measurements on exotic nuclides

The field stability of a mass spectrometer plays a crucial role in the accuracy of mass measurements. In the case of mass determination of short-lived nuclides with a Penning trap, major causes of fluctuations are temperature variations in the vicinity of the trap and pressure changes in the liquid helium cryostat of the superconducting magnet. Thus systems for the temperature and pressure stabilization of the Penning trap mass spectrometer ISOLTRAP at the ISOLDE facility at CERN have been installed. A reduction of the temperature and pressure fluctuations by at least an order of magnitude down to Δ T ≈ ± 5 mK and Δ p ≈ ± 5 Pa has been achieved, which corresponds to a relative magnetic field change of Δ B / B = 2.7 × 10 - 9 and 1.1 × 10 - 10 , respectively.

Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content.

The high mass measurement accuracy and precision available with recently developed mass spectrometers is increasingly used in proteomics analyses to confidently identify tryptic peptides from complex mixtures of proteins, as well as post-translational modifications and peptides from nonannotated proteins. To take full advantage of high mass measurement accuracy instruments, it is necessary to limit systematic mass measurement errors. It is well known that errors in m/z measurements can be affected by experimental parameters that include, for example, outdated calibration coefficients, ion intensity, and temperature changes during the measurement. Traditionally, these variations have been corrected through the use of internal calibrants (well-characterized standards introduced with the sample being analyzed). In this paper, we describe an alternative approach where the calibration is provided through the use of a priori knowledge of the sample being analyzed. Such an approach has previously been demonstrated based on the dependence of systematic error on m/z alone. To incorporate additional explanatory variables, we employed multidimensional, nonparametric regression models, which were evaluated using several commercially available instruments. The applied approach is shown to remove any noticeable biases from the overall mass measurement errors and decreases the overall standard deviation of the mass measurement error distribution by 1.2-2-fold, depending on instrument type. Subsequent reduction of the random errors based on multiple measurements over consecutive spectra further improves accuracy and results in an overall decrease of the standard deviation by 1.8-3.7-fold. This new procedure will decrease the false discovery rates for peptide identifications using high-accuracy mass measurements.

Present and future experiments with stored exotic nuclei at the FRS-ESR facility

High accuracy mass and lifetime measurements are performed with the combination of the in-flight separator FRS and the cooler-storage ring ESR at GSI. Exotic nuclei are produced via projectile fragmentation and fission at (400–900) MeV/u. This energy range is the basis for unique experimental conditions with bare and few-electron fragments and allows for the first time investigations for decay channels which are rare or strictly forbidden in neutral atoms. New experimental developments and data including the discovery of new isotopes are presented. The comparison of the experimental results with theoretical predictions indicates the potential for improvements of nuclear models. A new generation of experiments will be possible with the advent of the proposed international Facility for Antiproton and Ion Research (FAIR).

Systematic characterization of high mass accuracy influence on false discovery and probability scoring in peptide mass fingerprinting

Whereas the bearing of mass measurement error on protein identification is sometimes underestimated, uncertainty in observed peptide masses unavoidably translates to ambiguity in subsequent protein identifications. Although ongoing instrumental advances continue to make high accuracy mass spectrometry (MS) increasingly accessible, many proteomics experiments are still conducted with rather large mass error tolerances. In addition, the ranking schemes of most protein identification algorithms do not include a meaningful incorporation of mass measurement error. This article provides a critical evaluation of mass error tolerance as it pertains to false positive peptide and protein associations resulting from peptide mass fingerprint (PMF) database searching. High accuracy, high resolution PMFs of several model proteins were obtained using matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI–FTICR–MS). Varying levels of mass accuracy were simulated by systematically modulating the mass error tolerance of the PMF query and monitoring the effect on figures of merit indicating the PMF quality. Importantly, the benefits of decreased mass error tolerance are not manifest in Mowse scores when operating at tolerances in the low parts-per-million range but become apparent with the consideration of additional metrics that are often overlooked. Furthermore, the outcomes of these experiments support the concept that false discovery is closely tied to mass measurement error in PMF analysis. Clear establishment of this relation demonstrates the need for mass error-aware protein identification routines and argues for a more prominent contribution of high accuracy mass measurement to proteomic science.

Carbohydrate Analysis by Desorption Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

We report the use of desorption electrospray ionization hybrid Fourier transform ion cyclotron resonance mass spectrometry (DESI-FT-ICR-MS) for the analysis of carbohydrates. Spectra of neat carbohydrates are presented along with their mass measurement accuracies and limits of detection. Furthermore, a comparison is made between the analyses of O-linked glycans from mucin by DESI-FT-ICR-MS and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. Finally, glycans from mucin are identified by using the high mass measurement accuracy and tandem MS capabilities afforded by the hybrid FT-ICR-MS platform.

Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling

We have developed an efficient and robust high-pressure capillary LC-MS method for the identification of large numbers of metabolites in biological samples using both positive and negative ESI modes. Initial efforts focused on optimizing the separation conditions for metabolite extracts using various LC stationary phases in conjunction with multiple mobile-phase systems, as applied to the separation of 45 metabolite standards. The optimal mobile and stationary phases of those tested were determined experimentally (in terms of peak shapes, theoretical plates, retention of small, polar compounds, etc.), and both linear and exponential gradients were applied in the study of metabolite extracts from the cyanobacterium Cyanothece sp. ATCC 51142. Finally, an automated dual-capillary LC system was constructed and evaluated for the effectiveness and reproducibility of the chromatographic separations using the above samples. When coupled with a commercial LTQ-orbitrap MS, approximately 900 features were reproducibly detected from Cyanothece sp. ATCC 51142 metabolite extracts. In addition, 12 compounds were tentatively identified, based on accurate mass, isotopic distribution, and MS/MS information.

Emerging Technologies for Identification of Disinfection Byproducts: GC/FT−ICR MS Characterization of Solvent Artifacts

Water samples from a local water treatment plant were analyzed, using gas chromatography Fourier transform ion cyclotron resonance mass spectrometry (GC/FT-ICR MS), to identify potential disinfection byproducts (DBPs). Both liquid-liquid extraction (LLE) and solid-phase microextraction (SPME) techniques were used for sample preparation prior to GC/MS analyses. Based on the averaged mass measurement accuracy (MMA) of better than five parts-per-million (<5 ppm), multiple solvent artifacts were identified. It is shown that solventless SPME can be utilized to reduce potential interferences from solvent stabilizers. Six DBPs were detected and their molecular compositions were assigned at a high level of confidence. At the ppb concentration ranges and in the broadband mass spectral detection mode, internally calibrated mass spectra provided concurrent high resolution (resolving power M/deltaM50% > 30,000 at m/z values -110) and MMA of better than one part-per-million (MMA < 1 ppm). The use of thermochemical data, such as proton affinities, as a complementary tool to enhance analytical resolution is also demonstrated.

Indigo Carmine degradation by hypochlorite in aqueous medium monitored by electrospray ionization mass spectrometry

AbstractThe degradation of the dye Indigo Carmine by hypochlorite in aqueous solution was monitored by electrospray ionization mass spectrometry in the negative ion mode (ESI(—)‐MS). Hypochlorite was highly efficient in removing the color of aqueous solutions of the dye. ESI(—)‐MS monitoring showed that concomitant with the Indigo Carmine consumption two transient species appeared (detected as doubly charged anions) probably formed via a net insertion of two hydroxyl groups at the exocyclic CC bond followed by the incorporation of two (mainly) or one oxygen atoms at the indolic rings of the dye. Structures of these products were proposed based on the ESI(—)‐MS/MS data and high accuracy mass measurements. These two transient intermediates quickly decomposed, both in the condensed and in the gas phase, to yield mono‐charged anions. Based on these results, a route for the Indigo Carmine degradation by hypochlorite in aqueous solution has been proposed. Copyright © 2007 John Wiley &amp; Sons, Ltd.

Targeted Tandem Mass Spectrometry for High-Throughput Comparative Proteomics Employing NanoLC-FTICR MS with External Ion Dissociation

Targeted tandem mass spectrometry (MS/MS) is an attractive proteomic approach that allows selective identification of peptides exhibiting abundance differences, e.g., between culture conditions and/or diseased states. Herein, we report on a targeted LC-MS/MS capability realized with a hybrid quadrupole-7 tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer that provides data-dependent ion selection, accumulation, and dissociation external to the ICR trap, and a control software that directs intelligent MS/MS target selection based on LC elution time and m/z ratio. We show that the continuous on-the-fly alignment of the LC elution time during the targeted LC-MS/MS experiment, combined with the high mass resolution of FTICR MS, is crucial for accurate selection of targets, whereas high mass measurement accuracy MS/MS data facilitate unambiguous peptide identifications. Identification of a subset of differentially abundant proteins from Shewanella oneidensis grown under suboxic versus aerobic conditions demonstrates the feasibility of such approach.

Ion Mobility Spectrometry–Mass Spectrometry Performance Using Electrodynamic Ion Funnels and Elevated Drift Gas Pressures

The ability of ion mobility spectrometry coupled with mass spectrometry (IMS-MS) to characterize biological mixtures has been illustrated over the past eight years. However, the challenges posed by the extreme complexity of many biological samples have demonstrated the need for higher resolution IMS-MS measurements. We have developed a higher resolution ESI-IMS-TOF MS by utilizing high-pressure electrodynamic ion funnels at both ends of the IMS drift cell and operating the drift cell at an elevated pressure compared with that conventionally used. The ESI-IMS-TOF MS instrument consists of an ESI source, an hourglass ion funnel used for ion accumulation/injection into an 88 cm drift cell, followed by a 10 cm ion funnel and a commercial orthogonal time-of-flight mass spectrometer providing high mass measurement accuracy. It was found that the rear ion funnel could be effectively operated as an extension of the drift cell when the DC fields were matched, providing an effective drift region of 98 cm. The resolution of the instrument was evaluated at pressures ranging from 4 to 12 torr and ion mobility drift voltages of 16 V/cm (4 torr) to 43 V/cm (12 torr). An increase in resolution from 55 to 80 was observed from 4 to 12 torr nitrogen drift gas with no significant loss in sensitivity. The choice of drift gas was also shown to influence the degree of ion heating and relative trapping efficiency within the ion funnel.

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.

High-precision mass measurements for fundamental applications using highly-charged ions with SMILETRAP

The Penning trap mass spectrometer SMILETRAP takes advantage of highly-charged ions for high-accuracy mass measurements. In this paper recent mass measurements on Li and Ca ions are presented and their impact on fundamental applications discussed, especially the need for accurate mass values of hydrogen-like and lithium-like ions in the evaluation of the electron g-factor measurements in highly-charged ions is emphasized. Such experiments aim to test bound state quantum electrodynamics. Here the ionic mass is a key ingredient, which can be the limiting factor for the final precision.

Direct characterization of intact polypeptides by matrix‐assisted laser desorption electrospray ionization quadrupole Fourier transform ion cyclotron resonance mass spectrometry

We report the characterization of a recently introduced hybrid ionization source, matrix-assisted laser desorption electrospray ionization (MALDESI), coupled to a quadrupole Fourier transform ion cyclotron resonance mass spectrometry (QFT-ICR-MS) system. We first demonstrate the ability of MALDESI-QFT-ICR MS to directly analyze and provide high mass measurement accuracy (approximately 1 part-per-million) of a polypeptide using internal calibration. Second, we show the potential of MALDESI-QFT-ICR MS for the top-down characterization of multiply charged polypeptide cations. Finally, we demonstrate sub-femtomole detection limits in MALDESI-QFT-ICR MS using a combination of naturally occurring peptides and their respective stable isotope labeled forms. The results presented herein demonstrate the feasibility of several potential applications for MALDESI-QFT-ICR MS for the direct analysis of intact biological molecules.

Formation of ε-Formyllysine on Silver-stained Proteins: Implications for Assignment of Isobaric Dimethylation Sites by Tandem Mass Spectrometry

Considerable effort is focused presently on the detection and comprehensive assignment of post-translational modifications of proteins. Obviously attention must be paid to the possibility of chemical modifications that may occur to protein samples during sample handling and manipulation prior to analysis by tandem mass spectrometry. This is of particular concern when a modification is isobaric with the mass differential in common with a known post-translational analog. Here we provide evidence that silver staining protocols that use formaldehyde can result in epsilon-formylation of lysine residues. This modification is in fact isobaric with the important product of methyltransferases, epsilon,epsilon-dimethyllysine. Without exercising proper caution the analysis of silver-stained protein samples by mass spectrometry looking for dimethylation of lysine will yield a significant number of misassigned sites of modification. High accuracy measurements of the mass of the precursor ions and their fragments are required to eliminate this uncertainty. The occurrence of dimethylation of the epsilon-amino function of lysine residues has been reported often in histones. For histone samples excised from silver-stained gels, we found that most sites initially assigned to be dimethylated by automatic search engines under standard search parameters (100 ppm error tolerance) are actually in fact formylated. Caution must be exercised when data obtained from instruments unable to perform high accuracy mass measurements (better than 5 ppm) are to be interpreted.