Mass Spectrometric Performance Research Articles

Modelling mass analyzer performance with fields determined using the boundary element method

Computer modelling is widely used in the design of mass analysers to evaluate proposed designs and determine the effects of manufacturing imperfections. For quadrupole mass filters and ion traps, the models require accurate values of the electric field throughout the regions of the analyser in which ions travel. Most published results using models to predict mass analyser behaviour use electric fields computed with finite element (FE) or finite difference (FD) method. However, the boundary element method (BEM) is capable of achieving the same, or higher, accuracy with both computation times and memory requirements that are at least an order of magnitude less than those required by FE and FD methods. In this paper, electric field evaluation is performed using the BEM formulated in a manner described by previous workers; modifications to their method are described, which lead to higher accuracy field values. Simultaneous equation solution techniques are incorporated, which avoid solutions that are physically not realistic. The performance of linear quadrupole mass spectrometers with hyperbolic, circular and planar section electrodes has been determined using fields computed using these methods and compared with previous results obtained by alternative field computation techniques and with experiment. Behaviour of an ion trap mass spectrometer with circular symmetry has also been investigated. The results demonstrate that in each case using the BEM to determine the fields produces the observed behaviour.

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.

Mass Spectral Analysis of Neuropeptide Expression and Distribution in the Nervous System of the Lobster Homarus americanus

The lobster Homarus americanus has long served as an important animal model for electrophysiological and behavioral studies. Using this model, we performed a comprehensive investigation of the neuropeptide expression and their localization in the nervous system, which provides useful insights for further understanding of their biological functions. Using nanoLC ESI Q-TOF MS/MS and three types of MALDI instruments, we analyzed the neuropeptide complements in a major neuroendocrine structure, pericardial organ. A total of 57 putative neuropeptides were identified and 18 of them were de novo sequenced. Using direct tissue/extract analysis and bioinformatics software SpecPlot, we charted the global distribution of neuropeptides throughout the nervous system in H. americanus. Furthermore, we also mapped the localization of several neuropeptide families in the brain by high mass resolution and high mass accuracy mass spectrometric imaging (MSI) using a MALDI LTQ Orbitrap mass spectrometer. We have also compared the utility and instrument performance of multiple mass spectrometers for neuropeptide analysis in terms of peptidome coverage, sensitivity, mass spectral resolution and capability for de novo sequencing.

Ion trap mass analysis at high pressure: an experimental characterization

In recent years, it has become increasingly interesting to understand the performance of mass spectrometers at pressures much higher than those employed with conventional operating conditions. This interest has been driven by several influences, including demand for the development of reduced-power miniature mass spectrometers, desire for improved ion transfer into and through mass spectrometers, enhanced-yield preparative mass separations, and mass filtering at the atmospheric pressure interface. In this study, an instrument was configured to allow for the performance characterization of a rectilinear ion trap (RIT) at pressures up to 50 mtorr with air used as the buffer gas. The mass analysis efficiency, mass resolution, isolation efficiency, and collision-induced dissociation (CID) efficiency were evaluated at pressures ranging from 1 to 50 mtorr. The extent of degradation of mass resolution, isolation efficiency and ion stability as functions of pressure were characterized. Also, the optimal resonance ejection conditions were obtained at various pressures. Operations at 50 mtorr demonstrated improved CID efficiency in addition to peak widths of 2 and 5 m/z units (full width at half-maximum, FWHM) for protonated caffeine (m/z 195) and Ultramark (m/z 1521) respectively.

Accelerator Mass Spectrometry (AMS) 1977–1987

The eleventh Accelerator Mass Spectrometry (AMS 11) Conference took place in September 2008, the Thirtieth Anniversary of the first Conference. That occurred in 1978 after discoveries with nuclear physics accelerators in 1977. Since the first Conference there have now been ten further conferences on the development and applications of what has become known as AMS. This is the accepted acronym for the use of accelerators, together with nuclear and atomic physics techniques, to enhance the performance of mass spectrometers for the detection and measurement of rare long-lived radioactive elements such as radiocarbon. This paper gives an outline of the events that led to the first conference together with a brief account of the first four conferences before the introduction of the second generation of accelerator mass spectrometers at AMS 5.

Application of mass spectrometry in the analysis of polybrominated diphenyl ethers

This review summarized the applications of mass spectrometric techniques for the analysis of the important flame retardants polybrominated diphenyl ethers (PBDEs) to understand the environmental sources, fate and toxicity of PBDEs that were briefly discussed to give a general idea for the need of analytical methodologies. Specific performance of various mass spectrometers hyphenated with, for example, gas chromatograph, liquid chromatograph, and inductively coupled plasma (GC/MS, LC/MS, and ICP/MS, respectively) for the analysis of PBDEs was compared with an objective to present the information on the evolution of MS techniques for determining PBDEs in environmental and human samples. GC/electron capture negative ionization quadrupole MS (GC/NCI qMS), GC/high resolution MS (GC/HRMS) and GC ion trap MS (GC/ITMS) are most commonly used MS techniques for the determination of PBDEs. New analytical technologies such as fast tandem GC/MS and LC/MS become available to improve analyses of higher PBDEs. The development and application of the tandem MS techniques have helped to understand environmental fate and transformations of PBDEs of which abiotic and biotic degradation of decaBDE is thought to be one major source of Br(1-9)BDEs present in the environment in addition to direct loading from commercial mixtures. MS-based proteomics will offer an insight into the molecular mechanisms of toxicity and potential developmental and neurotoxicity of PBDEs.

The Effects of Entrance Fields on the Performance of Quadrupole Mass Spectrometers

The theoretical performance of quadrupole mass spectrometers has been studied by means of a new computer model, with particular reference to three-dimensional ion trajectories, both within the main filter and the entrance fields, including the effects of z-energy changes in the latter. It is shown that considerable improvements in acceptance area can be obtained by suitable modification of the entrance fields.

Comparison between the Matrices α-Cyano-4-hydroxycinnamic Acid and 4-Chloro-α-cyanocinnamic Acid for Trypsin, Chymotrypsin, and Pepsin Digestions by MALDI-TOF Mass Spectrometry

The performance of the recently developed 4-chloro-alpha-cyanocinnamic acid (Cl-CCA) matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) matrix was investigated in comparison to the most widely used matrix alpha-cyano-4-hydroxycinnamic acid (CHCA). For this purpose, in-solution digestions of standard proteins in the low femtomole range with the proteases trypsin, chymotrypsin, and pepsin were used as analytes. For all protein-protease combinations, Cl-CCA revealed to be highly superior in terms of number of identified peptides, obtained sequence coverages and peptide detection reproducibility. A deeper inspection of the detected peptide signals with regard to both physicochemical peptide properties (their isoelectric point) and mass spectrometric performance (signal-to-noise ratios and mass accuracies) showed that the progress achieved with Cl-CCA is due to the detection of numerous acidic to neutral peptides. Moreover, the higher Cl-CCA sensitivity allowed for the detection of numerous additional phosphopeptides, all of which were verified by means of MS/MS investigations. The occurrence of strong signals of doubly charged peptides which is exclusively observed for the Cl-CCA matrix can be traced back to the peptide amino-acid composition, that is, the presence of a high number of basic amino acids (Arg, Lys, and His) and is thus more pronounced for nontryptic protein digests. These observed improvements well agree with an increased protonation reactivity of Cl-CCA and are more pronounced with a decreasing level of protease specificity and decreasing sample amounts.

A method for assessing and maintaining the reproducibility of mass spectrometric analyses of complex samples

Direct injection mass spectrometric analysis of biological samples is potentially an attractive approach to the discovery of diagnostic patterns for specific pathophysiological conditions because of its speed and simplicity. Despite the possible benefits offered by such a method, its extensive application has been limited so far by several factors, including the inadequate reproducibility of the analytical results. We describe a method for monitoring and optimizing the performance of mass spectrometers used for biomarker discovery studies, based on the analysis of patterns of standardized spectral features. The method was successfully applied to maintaining spectral reproducibility during a multi-day analysis of hundreds of serum samples despite an ion source failure, which necessitated minor maintenance. The monitoring method allowed the early detection of that failure and the restoration of the spectral profiles after the system was restarted.

Orbitrap mass spectrometry: Instrumentation, ion motion and applications

Since its introduction, the orbitrap has proven to be a robust mass analyzer that can routinely deliver high resolving power and mass accuracy. Unlike conventional ion traps such as the Paul and Penning traps, the orbitrap uses only electrostatic fields to confine and to analyze injected ion populations. In addition, its relatively low cost, simple design and high space-charge capacity make it suitable for tackling complex scientific problems in which high performance is required. This review begins with a brief account of the set of inventions that led to the orbitrap, followed by a qualitative description of ion capture, ion motion in the trap and modes of detection. Various orbitrap instruments, including the commercially available linear ion trap-orbitrap hybrid mass spectrometers, are also discussed with emphasis on the different methods used to inject ions into the trap. Figures of merit such as resolving power, mass accuracy, dynamic range and sensitivity of each type of instrument are compared. In addition, experimental techniques that allow mass-selective manipulation of the motion of confined ions and their potential application in tandem mass spectrometry in the orbitrap are described. Finally, some specific applications are reviewed to illustrate the performance and versatility of the orbitrap mass spectrometers.

Breaking the Pumping Speed Barrier in Mass Spectrometry: Discontinuous Atmospheric Pressure Interface

The performance of mass spectrometers with limited pumping capacity is shown to be improved through use of a discontinuous atmospheric pressure interface (DAPI). A proof-of-concept DAPI interface was designed and characterized using a miniature rectilinear ion trap mass spectrometer. The interface consists of a simple capillary directly connecting the atmospheric pressure ion source to the vacuum mass analyzer region; it has no ion optical elements and no differential pumping stages. Gases carrying ionized analytes were pulsed into the mass analyzer for short periods at high flow rates rather than being continuously introduced at lower flow rates; this procedure maximized ion transfer. The use of DAPI provides a simple solution to the problem of coupling an atmospheric pressure ionization source to a miniature instrument with limited pumping capacity. Data were recorded using various atmospheric pressure ionization sources, including electrospray ionization (ESI), nano-ESI, atmospheric pressure chemical ionization (APCI), and desorption electrospray ionization (DESI) sources. The interface was opened briefly for ion introduction during each scan. With the use of the 18 W pumping system of the Mini 10, limits of detection in the low part-per-billion levels were achieved and unit resolution mass spectra were recorded.

Peptidomics: The integrated approach of MS, hyphenated techniques and bioinformatics for neuropeptide analysis

MS is currently one of the most important analytical techniques in biological and medical research. ESI and MALDI launched the field of MS into biology. The performance of mass spectrometers increased tremendously over the past decades. Other technological advances increased the analytical power of biological MS even more. First, the advent of the genome projects allowed an automated analysis of mass spectrometric data. Second, improved separation techniques, like nanoscale HPLC, are essential for MS analysis of biomolecules. The recent progress in bioinformatics is the third factor that accelerated the biochemical analysis of macromolecules. The first part of this review will introduce the basics of these techniques. The field that integrates all these techniques to identify endogenous peptides is called peptidomics and will be discussed in the last section. This integrated approach aims at identifying all the present peptides in a cell, organ or organism (the peptidome). Today, peptidomics is used by several fields of research. Special emphasis will be given to the identification of neuropeptides, a class of short proteins that fulfil several important intercellular signalling functions in every animal. MS imaging techniques and biomarker discovery will also be discussed briefly.

Peculiarities of the MX7304A monopole mass spectrometer performance in pulse counting mode

The peculiarities of the performance of the MX7304A monopole mass spectrometer in the pulse counting mode are considered. The advantages and drawbacks of the counting mode are discussed. A method for selecting the optimal voltage of a secondary-electron multiplier is described. A technique for correcting the detector signal in view of counting loss at high signal rates is proposed.

Mass Spectrometry and Peptide-based Vaccine Development

The development of new vaccines against pathogens is an important part of infectious disease control. In the last decade, a variety of proteins giving rise to naturally processed pathogen-derived antigenic peptides, representing B-cell and T-cell epitopes, have been characterized. Numerous candidate vaccines consisting of synthetic peptides are being designed and evaluated, with encouraging results. In this context, the application of mass spectrometry based on the isolation and identification of pathogen-derived peptides from the human leukocyte antigen (HLA) molecules is a major focus of peptide-based vaccine development. Dramatic improvements have been made in mass spectrometer performance for peptide sequencing in terms of increased sensitivity, the ability to rapidly obtain data-directed tandem mass spectra, and the accuracy of mass measurement. This review focuses on the efforts to identify T-cell epitopes for viral and microbial pathogens for directed vaccine development.

Capillary liquid chromatography combined with tandem mass spectrometry for the study of neurosteroids and oxysterols in brain

Neurosteroids and neurosterols are found in brain at low levels (ng/g–μg/g) against a high background of cholesterol (mg/g). As such their analysis can be challenging. Traditionally, these molecules have been analysed by gas chromatography (GC)–mass spectrometry (MS), however, the absence of molecular ions in GC–MS spectra, even from derivatised molecules, can make the discovery and identification of novel neurosteroids/sterols difficult. To avoid this scenario, liquid chromatography (LC) combined with desorption ionisation methods are employed. In this review we discuss the application of LC–MS and LC–tandem mass spectrometry (MS/MS) for the identification of neurosteroids/sterols, paying particular attention to the use of low-flow-rate LC to maximise chromatographic and mass spectrometric performance.

Metal particles produced by laser ablation for ICP–MS measurements

Pulsed laser ablation (266 nm) was used to generate metal particles of Zn and Al alloys using femtosecond (150 fs) and nanosecond (4 ns) laser pulses with identical fluences of 50 J cm −2. Characterization of particles and correlation with inductively coupled plasma mass spectrometer (ICP–MS) performance was investigated. Particles produced by nanosecond laser ablation were mainly primary particles with irregular shape and hard agglomerates (without internal voids). Particles produced by femtosecond laser ablation consisted of spherical primary particles and soft agglomerates formed from numerous small particles. Examination of the craters by white light interferometric microscopy showed that there is a rim of material surrounding the craters formed after nanosecond laser ablation. The determination of the crater volume by white light interferometric microscopy, considering the rim of material surrounding ablation craters, revealed that the volume ratio (fs/ns) of the craters on the selected samples was approximately 9 (Zn), 7 (NIST627 alloy) and 5 (NIST1711 alloy) times more ablated mass with femtosecond pulsed ablation compared to nanosecond pulsed ablation. In addition, an increase of Al concentration from 0 to 5% in Zn base alloys caused a large increase in the diameter of the particles, up to 65% while using nanosecond laser pulses. When the ablated particles were carried in argon into an ICP–MS, the Zn and Al signals intensities were greater by factors of ∼50 and ∼12 for fs versus ns ablation. Femtosecond pulsed ablation also reduced temporal fluctuations in the 66Zn transient signal by a factor of 10 compared to nanosecond laser pulses.

Collection and storage of CO2 for 13C analysis: an application to separate soil CO2 efflux into root‐ and soil‐derived components

Soil surface CO2 efflux is comprised of CO2 from (i) root respiration and rhizosphere microbes and (ii) heterotrophic respiration from the breakdown of soil organic matter (SOM). This efflux may be partitioned between these sources using delta13C measurements. To achieve this, continuous flow isotope ratio mass spectrometry can be used and, in conjunction with 10 mL septum-capped vials, large numbers of samples may be analysed using a Finnigan MAT Delta(plus)XP interfaced to a Gas Bench II. Here we describe a number of advances to facilitate such work, including: (i) a technique for monitoring mass spectrometer performance, (ii) improvements to sample storage, and (iii) a gas-handling system for incubating and sampling the CO2 derived from roots and soils. Mass spectrometer performance was monitored using an automated refillable vial. Compressed air analysed with this system had mean delta13C of -9.61 +/- 0.16 per thousand (+/- 1sigma, n = 28) collected over four runs. Heating the butyl rubber septa used to seal the vials at 105 degrees C for 12 h improved the sample storage. After air transportation over 12 days, the isotope composition of the CO2 at ambient concentrations was unchanged (before: -35.2 +/- 0.10 per thousand, n = 4; after: -35.3 +/- 0.10 per thousand, n = 15); without heat treatment of the septa the CO2 became slightly enriched (-35.0 +/- 0.14 per thousand, n = 15). The linearity of the Gas Bench II was found to decline above 8000 micromol CO2 mol(-1). To stay within a linear range and to allow the incubation of soil and root material we describe a gas-handling system based around a peristaltic pump. Finally, we demonstrate these methods by growing a C-4 grass (Guinea grass, Panicum maximum Jacq.) in a C-3 soil. Root respiration was found to contribute between 5 and 22% to the soil surface CO2 efflux. These methodologies will facilitate experiments aimed at measuring the isotopic composition of soil-derived CO2 across a range of ecological applications.

Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach

We describe the application of LC-MS without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and suboxic conditions. LC-MS/MS was used to initially identify peptide sequences, and LC-FTICR was used to confirm these identifications as well as measure relative peptide abundances. 2343 peptides covering 668 proteins were identified with high confidence and quantified. Among these proteins, a subset of 56 changed significantly using statistical approaches such as statistical analysis of microarrays, whereas another subset of 56 that were annotated as performing housekeeping functions remained essentially unchanged in relative abundance. Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis was transitioned from aerobic to suboxic conditions.

Fabrication of enclosed SU-8 tips for electrospray ionization-mass spectrometry

We describe a novel electrospray tip design for MS which is fabricated completely out of SU-8 photoepoxy. A three-layer SU-8 fabrication process provides fully enclosed channels and tips. The tip shape and alignment of all SU-8 layers is done lithographically and is therefore very accurate. Fabrication process enables easy integration of additional fluidic functions on the same chip. Separation channels can be made with exactly the same process. Fluidic inlets are made in SU-8 during the fabrication process and no drilling or other postprocessing is needed. Channels have been fabricated and tested in the size range of 10 microm x 10 microm-50 microm x 200 microm. Mass spectrometric performance of the tips has been demonstrated with both pressure-driven flow and EOF. SU-8 microtips have been shown to produce stable electrospray with EOF in a timescale of tens of minutes. With pressure driven flow stable spray is maintained for hours. Taylor cone was shown to be small in volume and well defined even with the largest channel cross section. The spray was also shown to be well directed with our tip design.

Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap

Mass accuracy is a key parameter of mass spectrometric performance. TOF instruments can reach low parts per million, and FT-ICR instruments are capable of even greater accuracy provided ion numbers are well controlled. Here we demonstrate sub-ppm mass accuracy on a linear ion trap coupled via a radio frequency-only storage trap (C-trap) to the orbitrap mass spectrometer (LTQ Orbitrap). Prior to acquisition of a spectrum, a background ion originating from ambient air is first transferred to the C-trap. Ions forming the MS or MS(n) spectrum are then added to this species, and all ions are injected into the orbitrap for analysis. Real time recalibration on the "lock mass" by corrections of mass shift removes mass error associated with calibration of the mass scale. The remaining mass error is mainly due to imperfect peaks caused by weak signals and is addressed by averaging the mass measurement over the LC peak, weighted by signal intensity. For peptide database searches in proteomics, we introduce a variable mass tolerance and achieve average absolute mass deviations of 0.48 ppm (standard deviation 0.38 ppm) and maximal deviations of less than 2 ppm. For tandem mass spectra we demonstrate similarly high mass accuracy and discuss its impact on database searching. High and routine mass accuracy in a compact instrument will dramatically improve certainty of peptide and small molecule identification.