Automatic internal calibration in liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry of protein digests

Accurately measured peptide masses can be used for large-scale protein identification from bacterial whole-cell digests as an alternative to tandem mass spectrometry (MS/MS) provided mass measurement errors of a few parts-per-million (ppm) are obtained. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) routinely achieves such mass accuracy either with internal calibration or by regulating the charge in the analyzer cell. We have developed a novel and automated method for internal calibration of liquid chromatography (LC)/FTICR data from whole-cell digests using peptides in the sample identified by concurrent MS/MS together with ambient polydimethylcyclosiloxanes as internal calibrants in the mass spectra. The method reduced mass measurement error from 4.3 +/- 3.7 ppm to 0.3 +/- 2.3 ppm in an E. coli LC/FTICR dataset of 1000 MS and MS/MS spectra and is applicable to all analyses of complex protein digests by FTICRMS.     

Visualization and application of amino acid retention coefficients obtained from modeling of peptide retention

We introduce a method for data inspection in liquid separations of peptides using amino acid retention coefficients and their relative change across experiments. Our method allows for the direct comparison between actual experimental conditions, regardless of sample content and without the use of internal standards. The modeling uses linear regression of peptide retention time as a function of amino acid composition. We demonstrate the pH dependency of the model in a control experiment where the pH of the mobile phase was changed in controlled way. We introduce a score to identify the false discovery rate on peptide spectrum match level that corresponds to the set of most robust models, i.e. to maximize the shared agreement between experiments. We demonstrate the method utility in reversed‐phase liquid chromatography using 24 datasets with minimal peptide overlap. We apply our method on datasets obtained from a public repository representing various separation designs, including one‐dimensional reversed‐phase liquid chromatography followed by tandem mass spectrometry, and two‐dimensional online strong cation exchange coupled to reversed‐phase liquid chromatography followed by tandem mass spectrometry, and highlight new insights. Our method provides a simple yet powerful way to inspect data quality, in particular for multidimensional separations, improving comparability of data at no additional experimental cost.     

Toward standardization of quality assessment in laboratory medicine by using the same matrix samples for both internal and external quality assessments

The main purpose of quality assurance procedures in clinical laboratories is to ensure that test results are appropriate to maintain excellence in the diagnosis, monitoring, and treatment of disease. However, in current practice, no standardized procedure or frequency for the evaluation of methods exists, particularly in external quality assessment. Furthermore, different quality control materials are typically used for internal and external quality assessment. To overcome these discrepancies, we used samples with the same matrix for both internal and external quality assessments of a group test performed in our laboratory. We then calculated total error using real bias (target value obtained by reference method) and the imprecision of each test and compared our results with the total error allowable, derived from biological variation data. We suggest that the strategy of using the same matrix samples for both internal and external quality assessment is cost-effective, can be readily used by staff, and will facilitate the standardization of quality control in clinical laboratories.     

Accurate inertias for large-amplitude motions: improvements on prevailing approximations

We present a simple yet accurate method for the calculation of effective moments of inertia for large-amplitude low-frequency internal motions in molecules. Our technique makes use of the quantum-mechanical kinetic energy operator developed within the internal coordinate path Hamiltonian formalism, with the imposition of Eckart conditions on the molecular frame to separate the internal motion from overall molecular rotation. Numerical results are presented for several molecules possessing internal large-amplitude motions. These results are compared with those obtained from approximate analytic formulas proposed by Pitzer. We also give detailed examples where the conventional approximations in the current literature are not applicable for describing a single large-amplitude motion. Our straightforward algorithm yields results more accurate than those of Pitzer's method, especially for molecules with asymmetric internal rotors.     

Rotational symmetry of the molecular potential energy in the Cartesian coordinates

We consider the molecular Born-Oppenheimer potential energy as a function of atomic Cartesian coordinates and discuss the non-stationary Hessian properties arising due to rotational symmetry. A connection with the extended Hessian theory is included. New applications of Cartesian representation for examining and correcting raw numerical Hessian data and a simple formulation of harmonic vibrational analysis of partially optimized systems are proposed. Exemplary calculations for the porphyrin molecule with an internal proton transfer are reported. We also develop the normal transformation method to incorporate the rotational symmetry into the approximate analytical potentials, which are parametrized in the Cartesian coordinates. The transformation converts the coordinates from the space fixed frame to the frame which translates and rotates with the molecule and is determined by the Eckart conditions. New simple analytical formulas for the first and second derivatives of the transformed potential are derived. This fast method can be used to calculate the potential and its derivatives in the simulations of chemical reaction dynamics in the space fixed Cartesian frame without the need to constrain the molecular rotation or to define the local non-redundant internal coordinates.     

Wavelet-accelerated Monte Carlo sampling of polymer chains

We introduce a new method for coarse-graining polymer chains, based on the wavelet transform, a multiresolution data analysis technique. This method, which assigns a cluster of particles to a coarse-grained bead located at the center of mass of the cluster, reduces the complexity of the problem significantly by dividing the simulation into several stages, each with a small fraction of the number of beads in the overall chain. At each stage, we compute the distributions of coarse-grained internal coordinates as well as potential functions required for subsequent simulation stages. We show that, with this wavelet-accelerated Monte Carlo method, coarse-grained Gaussian and self-avoiding random walks can reproduce results obtained from atomistic simulations to a high degree of accuracy in orders of magnitude less time. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 897–910, 2005     

Nanosecond to microsecond protein dynamics probed by magnetic relaxation dispersion of buried water molecules

Large-scale protein conformational motions on nanosecond-microsecond time scales are important for many biological processes, but remain largely unexplored because of methodological limitations. NMR relaxation methods can access these time scales if protein tumbling is prevented, but the isotropy required for high-resolution solution NMR is then lost. However, if the immobilized protein molecules are randomly oriented, the water 2H and 17O spins relax as in a solution of freely tumbling protein molecules, with the crucial difference that they now sample motions on all time scales up to approximately 100 micros. In particular, the exchange rates of internal water molecules can be determined directly from the 2H or 17O magnetic relaxation dispersion (MRD) profile. This possibility opens up a new window for characterizing the motions of individual internal water molecules as well as the large-scale protein conformational fluctuations that govern the exchange rates of structural water molecules. We introduce and validate this new NMR method by presenting and analyzing an extensive set of 2H and 17O MRD data from cross-linked gels of two model proteins: bovine pancreatic trypsin inhibitor and ubiquitin. We determine residence times and order parameters of four internal water molecules in these proteins and show that they are quantitatively consistent with the information available from crystallography and solution MRD. We also show how slow motions of side-chains bearing labile hydrogens can be monitored by the same approach. Proteins of any size can be studied at physiological hydration levels with this method.     

Harmonized internal quality aspects of a multi-residue method for determination of forty-six semivolatile compounds in water by stir-bar-sorptive extraction–thermal desorption gas chromatography–mass spectrometry

Three main aspects of internal quality—internal method validation, internal quality control (IQC), and sample result uncertainty—have been established for a multi-residue method for determination of 46 organic micropollutants (pesticides and polycyclic aromatic hydrocarbons) in water by stir-bar-sorptive extraction (SBSE) and thermal desorption (TD) coupled to capillary gas chromatography–mass spectrometry (GC–MS). From data obtained with increasing time, the process mean and standard deviation were used to harmonize the internal quality statistics. The relationship between these statistics and the hydrophobicity of the compounds was evaluated.     

A fast high throughput method for the determination of acidity constants by capillary electrophoresis. 3. Basic internal standards

A set of 25 monoprotic bases is proposed as internal standards for pK(a) determination by capillary electrophoresis. The pK(a) of the bases is determined and compared with available literature data. The capillary electrophoresis internal standard method offers numerous advantages over other typical methods for pK(a) determination, especially of analysis time and buffer preparation. However, it requires disposing of appropriate standards with reference pK(a) value. The set of bases established in this work together with the set of acids previously established provide a reference set of compounds with well-determined acidity constants that facilitate the process of selecting appropriate internal standards for fast pK(a) determination by capillary electrophoresis in high throughput screening of pharmaceutical drugs. In addition, the performance of the method when acidic internal standards are used for the determination of acidity constants of basic internal standards has also been tested. Although higher errors may be expected in this case, good agreement is observed between determined and literature values. These results indicate that in most cases structural similarity between the analyte and the internal standard might not be an essential requirement in the internal standard method.     

Topological coarse graining of polymer chains using wavelet-accelerated Monte Carlo. I. Freely jointed chains

We introduce a new, topologically-based method for coarse-graining polymer chains. Based on the wavelet transform, a multiresolution data analysis technique, this method assigns a cluster of particles to a coarse-grained bead located at the center of mass of the cluster, thereby reducing the complexity of the problem by dividing the simulation into several stages, each with a fraction of the number of beads as the overall chain. At each stage, we compute the distributions of coarse-grained internal coordinates as well as potential functions required for subsequent simulation stages. In this paper, we present the basic algorithm, and apply it to freely jointed chains; the companion paper describes its applications to self-avoiding chains.     

Conformational fluctuations affect protein alignment in dilute liquid crystal media

The discovery of dilute liquid crystalline media to align biological macromolecules has opened many new possibilities to study protein and nucleic acid structures by NMR spectroscopy. We inspect the basic alignment phenomenon for an ensemble of protein conformations to deduce relative contributions of each member to the residual dipolar coupling signals. We find that molecular fluctuations can affect the alignment and discover a resulting emphasis of certain conformations. However, the internal fluctuations are largely uncorrelated with those of the alignment, implying that proteins have liquidlike molecular surfaces. Furthermore, we consider the implications of a dynamic bias to structure determination using data from the weak alignment method.     

The Choice of Internal Standards for Measuring Volatile Pollutants in Water

54 volatile pollutants have been examined by static headspace-gas chromatography-mass selective detection in order to find the proper internal standard for each of the pollutants examined. The applicability of the internal standards has been assessed mathematically. For modelling, we prepared 2 × 4 × 4 solutions using blank water with added sodium sulphate and humic acid at four different concentrations for each. These solutions were spiked with two different concentrations of dilute standard solutions. We also examined 44 real water samples for traces of the 54 volatile pollutants, spiking them with dilute standard solutions. The results of a single measurement were 54 quotients for relative extraction efficiency: the area of the pollutant divided by the corresponding area of the spiked blank water measurement. For each pair of pollutants, the Pearson correlation coefficients were calculated for both the model and real water samples. We regarded two pollutants as being the same, if their Pearson correlation coefficient was greater than 0.95. Among similar pollutants we selected candidates for being suitable internal standards based on the highest correlation coefficients. We found, that five compounds are sufficient to cover 49 pollutants. Two pollutants did not exhibit a matrix effect and for these only the external calibration method can be used. For three pollutants, special considerations apply.The measurement data generally verified that structurally similar compounds have high correlation coefficients, but there were exceptions among similar compounds and unexpected similarities were also found. Nothing was found in the literature on determining the proper internal standard using Pearson correlation coefficients.     

How to detect internal motion by homonuclear NMR

NOESY and ROESY cross-peak intensities depend on internuclear distances and internal motion. Internal motion is usually ignored, and NOESY cross-peak intensities are interpreted in terms of internuclear distances only. Off-resonance ROESY experiments measure a weighted average of NOE and ROE. The weight can be described and experimentally set by an angle theta;. For large enough molecules, NOE and ROE have opposite signs. Therefore, each cross-peak intensity becomes zero for an angle theta;(0). For any sample, the maximum angle theta;(0) is determined by the overall motion of the molecule. Smaller theta;(0) values reflect the angular component of internal motions. Because individual cross-peaks are analyzed, the method evaluates internal motions of individual H,H vectors. The reduction of theta;(0) is largest for internal motions on a time scale of 100-300 ps. The sensitivity of theta;(0) for internal motions decreases with increasing molecular weight. We estimate that detecting internal motions will be practicable for molecules up to about 15 kDa. We describe a protocol to measure theta;(0) from a series of off-resonance ROESY spectra. For such a series, we describe the choice of experimental parameters, a procedure to extract theta;(0) from the raw data, and the interpretation of theta;(0) in terms of internal motions. In the small protein BPTI, we analyzed 75 cross-peaks. The precision of theta;(0) was 0.25 degrees, as compared to typical reductions of theta;(0) of 3 degrees. We found a well-defined maximum theta;(0) for cross-peaks in rigid parts of the molecule, which reflects the overall motion of the molecule. For BPTI, also many structurally important long-range cross-peaks appear rigid. The lower theta;(0) values of long-range contacts involving methyl groups are consistent with methyl rotation on the 25-ps time scale. The lower theta;(0) values of the flexible C-terminus and of flexible side chains translate into upper limits for the angular order parameter of 0.4 and 0.5-0.8, respectively. Off-resonance ROESY can monitor internal motions of H,H contacts that are used in a structure calculation. Because no isotope labeling is needed, off-resonance ROESY can be used to detect internal motions in a wide range of natural products.     

Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules

We propose a rigorous method for removing rigid-body motions from a given molecular dynamics trajectory of a flexible macromolecule. The method becomes exact in the limit of an infinitesimally small sampling step for the input trajectory. In a recent paper [G. Kneller, J. Chem. Phys. 128, 194101 (2008)], one of us showed that virtual internal atomic displacements for small time increments can be derived from Gauss' principle of least constraint, which leads to a rotational superposition problem for the atomic coordinates in two consecutive time frames of the input trajectory. Here, we demonstrate that the accumulation of these displacements in a molecular-fixed frame, which evolves in time according to the virtual rigid-body motions, leads to the desired trajectory for internal motions. The atomic coordinates in the input and output trajectory are related by a roto-translation, which guarantees that the internal energy of the molecule is left invariant. We present a convenient implementation of our method, in which the accumulation of the internal displacements is performed implicitly. Two numerical examples illustrate the difference to the classical approach for removing macromolecular rigid-body motions, which consists of aligning its configurations in the input trajectory with a fixed reference structure.     

Comparison of high-performance liquid chromatography with electrochemical detection and gas chromatography-mass fragmentography for the assay of salsolinol, dopamine and dopamine metabolites in food and beverage samples

High-performance liquid chromatography with electrochemical detection (HPLC-ED) and combined gas chromatography--mass spectrometry in the single-ion monitoring mode (GC--MS-SIM) have been used for the determination of salsolinol, dopamine, 3,4-dihydroxyphenylacetic acid, 3,4-dihydroxyphenylethanol and norepinephrine in a selection of food and beverage samples. The unique specificity of the SIM mode allows a simple one-step extraction to be used even for complex sample matrices. We have been able to demonstrate the quantitative and qualitative advantages offered by GC--MS over HPLC--ED by direct comparison of the chromatographic data obtained. We demonstrate that the specificity of SIM and the benefits offered by the incorporation of deuterated internal standards make GC--MS-SIM the method of choice for valid identification and precise quantitation of salsolinol, dopamine and dopamine metabolites in a complex sample matrix.     

Optimization of carbohydrate silylation for gas chromatography

We developed and optimized a new carbohydrate mono- and disaccharides silylation reaction, replacing pyridine and requiring lower reaction temperature and less time. Our method consists of three basic steps. The first one is oxime formation, the second one silylate derivative and the last one gas chromatography separation and quantification with an internal standard. We evaluated several solvents, including acetonitrile, hydroxylamine and aniline. We found aniline to be the best reaction media for oxime formation with hydroxylamine hydrochloride. Among silylation agents we found N,O-bis(trimethyl)trifluoroacetamide (BSTFA) was the most efficient. Together these reagents favored both a short analysis time and fewer by-products. We evaluated the method with model solutions containing: arabinose and co-eluting xylose, fructose, glucose, sucrose and salicin (internal standard) and found it suitable for processed food analysis.     

HPLC determination of (+)-pseudoephedrine and (-)-ephedrine in Japanese herbal medicines containing Ephedra herb using solid-phase extraction

We developed a rapid and simple HPLC method combined with solid-phase extraction (SPE) for quantitative analysis of (+)-pseudoephedrine (PEP) and (-)-ephedrine (EP) in Japanese herbal (Kampo) medicines such as Kakkon-to, Sho-seiryu-to, Goshaku-san and Bofu-tsusho-san. SPE was performed on TOYOPAK IC-SP M containing propylsulfonic groups. Determination of PEP and EP was carried out using ion-pair reversed-phase HPLC with sodium dodecyl sulfate. N-Benzyldiethylamine was used as an internal standard. The analytical procedure was validated with regard to specificity, linearity, accuracy, and precision. These data suggest that the analytical method developed in this study is useful for quantitative analysis of PEP and EP in various formulations of Kampo medicine containing Ephedra herb.     

Application of a new AMIQAS computer program for integrated quality control, method evaluation and proficiency testing

Summary The computer program AMI - Quality Assessment Scheme (AMIQAS) was designed to give easy statistical management of analytical data in relation to method evaluation, internal quality control and proficiency testing. The program is designed in accordance with the recommendation of the ISO 5725 guideline and other official recommendations. The program consists of a database, test for outliers, statistics and graphs for evaluation of an analytical method for chemical, biological and environmental analysis, different control charts to be used in day-to-day internal quality control (Shewhart charts and z-charts). Finally the program has facilities to perform proficiency testing (also called external quality control) and produce the relevant evaluation reports for the documentation of method performance and quality control of results of measurements. The present paper demonstrates the applicability of the AMIQAS program for integrated method evaluation, internal quality control and proficiency testing using the determination of the concentration of lead in human whole blood as the numerical example.     

FluClass: A novel algorithm and approach to score and visualize the phylogeny of the influenza virus using mass spectrometry

A novel computer algorithm FluClass has been developed to facilitate the phylogenetic classification of influenza virus using mass spectral data. FluClass accepts a DNA or protein-based phylogenetic tree as input and generates theoretical peptide mass lists for each node. An experimental mass spectrum from an influenza virus protein digest is then placed onto the phylogenetic tree using a novel random resampling function (Z-score) that allows the scoring of spectrum against both internal and leaf nodes. Testing of the algorithm using hemagglutinin protein sequences from human-host influenza viruses showed that the Z-score performs comparably to the Profound scoring method for the scoring of leaf nodes and is substantially better at scoring internal nodes. Scoring of internal nodes allows colorizations of nodes of the phylogenetic tree enabling the classification of the query spectrum to be rapidly visualized. Finally we demonstrate the utility of FluClass on experimental spectra from six strains. Given that mass spectrometry data can be generated rapidly for influenza virus proteins, FluClass provides a fast and direct method for phylogenetic analysis of influenza proteins.