High mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry

Important factors that limit the mass measurement accuracy from a mass spectrometer are related to (1) the type of mass analyzer used and (2) the data processing/calibration methods used to obtain mass values from the raw data. Here, two data processing methods are presented that correct for systematic deviations when the mass of ions is measured using a time-of-flight (TOF) mass spectrometer. The first fitting method is one where m/z values are obtained from fitting peak distributions using double Gaussian functions. A second calibration method takes into account the slight nonlinear response of the TOF analyzer in addition to the drift in the calibration over time. Using multivariate regression, both of these two effects can be corrected for using a single calibration formula. Achievable performance was evaluated with a trypsin digestion of serum albumin and proteins from the organism D. radiodurans that was analyzed using gradient reversed-phase liquid chromatography combined with an electrospray ionization orthogonal TOF mass spectrometer. The root-mean-square deviation between the theoretical and experimental m/z values for serum albumin tryptic peptides was found to be 8 ppm using the double Gaussian-multivariate method compared to 29 ppm determined using linear calibration and normal peak centroiding. An advantage of the methods presented here is that no calibrant compounds need to be added to the mobile phase, thereby avoiding interference effects and signal suppression of analytes.     

Polarity switching accurate mass measurement of pharmaceutical samples using desorption electrospray ionization and a dual ion source interfaced to an orthogonal acceleration time-of-flight mass spectrometer

A novel approach for the rapid, accurate mass analysis of pharmaceutical solid, liquid, and cream formulations using desorption electrospray ionization (DESI) is described. The method is based on polarity switching and real-time accurate mass measurement in an orthogonal acceleration time-of-flight mass spectrometer fitted with a dual-inlet electrospray ion source. Infusion of a reference compound into one inlet provides a single-point "lock mass" for accurate mass measurement. The other inlet sprays solvent at the sample being investigated using DESI. Minimal sample preparation was required. Results demonstrate the ability to acquire simultaneously positive and negative accurate mass DESI data within the same acquisition, thus negating the need for repeat analysis in each ion mode. In this paper, drugs that preferentially ionize in a particular mode depending on their physiochemical properties are presented. Mass accuracy to within 2 mTh was obtained for all drugs sampled.     

Analysis of megadalton ions using cryodetection MALDI time-of-flight mass spectrometry

Presented are initial results from the first commercially available matrix-assisted laser desorption/ionization time-of-flight mass spectrometer specifically designed for the sensitive detection of very high mass ions (macromizer, Comet AG). This new instrument utilizes a 16-element superconducting tunnel junction detector coupled with a fully adjustable gimbal-mounted ion source/focusing region that allows unparalleled sensitivity for detection of singly charged high molecular weight ions. Using this new technology, the singly charged ions in the megadalton region are detected from immunoglobulin M and von Willebrand factor proteins. This detector technology also measures the kinetic energy of the particles impacting the detector, which can be correlated to the charge of the particles. Immunoglobulin G and streptavidin were used to demonstrate the ability of the macromizer instrument to detect high-mass ions and to discern the charge state of the ions.     

Optically timed submillimeter time-of-flight mass spectrometry

We demonstrate that using intense femtosecond laser pulses to optically time ion flight can lead to a miniature time-of-flight mass spectrometer. After laser ionization, the molecular ion is accelerated by a static electric field and detected using a second, delayed laser pulse. The relative positions of the two laser foci determine the ion flight distance while the time separation of the laser pulses fixes the ion flight time. We mass-resolve CS(2) or C(6)H(6) isotopes after a flight distance of 360 microm using either double ionization or Coulomb explosion detection.     

Profiling and characterizing skin ceramides using reversed-phase liquid chromatography-quadrupole time-of-flight mass spectrometry

An LC-MS based method for the profiling and characterization of ceramide species in the upper layer of human skin is described. Ceramide samples, collected by tape stripping of human skin, were analyzed by reversed-phase liquid chromatography coupled to high-resolution quadrupole time-of-flight mass spectrometry operated in both positive and negative electrospray ionization mode. All known classes of ceramides could be measured in a repeatable manner. Furthermore, the data set showed several undiscovered ceramides, including a class with four hydroxyl functionalities in its sphingoid base. High-resolution MS/MS fragmentation spectra revealed that each identified ceramide species is composed of several skeletal isomers due to variation in carbon length of the respective sphingoid bases and fatty acyl building blocks. The resulting variety in skeletal isomers has not been previously demonstrated. It is estimated that over 1000 unique ceramide structures could be elucidated in human stratum corneum. Ceramide species with an even and odd number of carbon atoms in both chains were detected in all ceramide classes. Acid hydrolysis of the ceramides, followed by LC-MS analysis of the end-products, confirmed the observed distribution of both sphingoid bases and fatty acyl groups in skin ceramides. The study resulted in an accurate mass retention time library for targeted profiling of skin ceramides. It is furthermore demonstrated that targeted data processing results in an improved repeatability versus untargeted data processing (72.92% versus 62.12% of species display an RSD < 15%).     

Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry

Desorption/ionization on silicon (DIOS) tandem time-of-flight (TOF/TOF) mass spectrometry (MS) provides high accuracy and significant fragmentation information, particularly in the characterization of biomolecules. DIOS TOF/TOF offers a high-throughput surface-based ionization platform as well as complete fragmentation through high collision energies. The absence of matrix interference in DIOS allows for the MS and MS/MS analysis of small molecules well below m/z 300. In addition, sample preparation is minimal, and the DIOS chips can be stored and reanalyzed for fragmentation information or accurate mass measurements. The combined benefits of robustness, minimal sample preparation, good sensitivity, high throughput, and sequencing capability make DIOS TOF/TOF a powerful tool for small molecule characterization and protein identification.     

Application of time-of-flight aerosol mass spectrometry for the online measurement of gaseous molecular iodine

Here we present a new application of a time-of-flight aerosol mass spectrometer (TOF-AMS) for the measurement of atmospheric trace gases in real-time. Usually, TOF-AMS instruments are not sensitive to gas-phase species due to the aerodynamic particle focusing inlet system which reduces the gas phase species by a factor of about 10(7) relative to the particle phase. This efficient removal of the gas phase and the resulting high relative enrichment of particles is one reason for the very high sensitivity of TOF-AMS instruments for particle phase compounds (detection limits in the sub-μg/m(3)-range for online measurements with 1 min integration time), which allows application of the instruments even under clean atmospheric conditions. Here we use artificially generated particles as sampling probes to transfer selected atmospheric trace gases into the particle phase before entering the AMS (gaseous compound trapping in artificially generated particles-AMS, GTRAP-AMS). The sampling probe particles are mixed with the gaseous analytes upstream of the TOF-AMS in a 0.5 L flow tube. As an exemplary application of the method, the measurement of trace levels of gaseous molecular iodine is demonstrated. α-Cyclodextrin (α-CD/NH(4)Br) particles are used as selective sampling probes to transfer molecular iodine into the AMS. A detection limit in the subparts-per-billion (sub-ppb) range was achieved. The method was compared to a recently developed off-line method that combines denuder sampling of gaseous I(2) and gas chromatography/mass spectrometry (GC/MS) analysis. To demonstrate the usability of the method, temporally resolved I(2) emission profiles from a brown algae species (Laminaria saccharina) under exposure of ambient ozone levels were investigated. Total I(2) release rates of 36.5 pmol min(-1) grams fresh weight (gFW)(-1) at 100 pbb O(3) and 33.4 pmol min(-1) gFW(-1) at 50 ppb O(3) were obtained within the first hour of ozone exposure.     

Sequence confirmation of modified oligonucleotides using chemical degradation, electrospray ionization, time-of-flight, and tandem mass spectrometry

We report the sequencing of highly modified oligonucleotides containing a mixture of 2'-deoxy, 2'-fluoro, 2'-O-methyl, abasic, and ribonucleotides. The passenger and guide strands each containing 48% and 86% of modified nucleotides, respectively, are representative sequences of synthetic short interfering RNAs (siRNAs). We describe herein the sequence confirmation of both strands using a series of robust chemical reactions, followed by analysis via ESI-TOF and ion trap mass spectrometry (ITMS). The following method enables the rapid sequence confirmation of highly modified oligonucleotides.     

On-chip proteolytic digestion and analysis using "wrong-way-round" electrospray time-of-flight mass spectrometry

Rapid protein digestion and analysis using a hybrid microchip nanoelectrospray device and time-of-flight mass spectrometry detection are reported. The device consists of a planar glass chip with microfabricated channels coupled to a disposable nanospray emitter. Reactions between substrate and enzyme (trypsin), mixed off-chip and then immediately loaded into a sample reservoir on the device, are monitored in real time following the onset of electrospray. Protein cleavage products are determined at the optimum pH for generating tryptic fragments, directly from the digestion buffer using "wrong-way-round" electrospray, i.e., monitoring (MH)+ ions from basic solutions. Intense tryptic peptide ions are observed within a few minutes following sample loading on the microchip. Proteins were identified from low femtomole or even attomole quantities of analyte/spectrum using peptide mass fingerprinting, loading 0.1-2 pmol/microL of sample on the chip. The sequence coverage for analyzed proteins ranged from 70 to 95%. The rapid analysis of human hemoglobin is demonstrated using the technique.     

Dynamically multiplexed ion mobility time-of-flight mass spectrometry

Ion mobility spectrometry-time-of-flight mass spectrometry (IMS-TOFMS) has been increasingly used in analysis of complex biological samples. A major challenge is to transform IMS-TOFMS to a high-sensitivity, high-throughput platform, for example, for proteomics applications. In this work, we have developed and integrated three advanced technologies, including efficient ion accumulation in an ion funnel trap prior to IMS separation, multiplexing (MP) of ion packet introduction into the IMS drift tube, and signal detection with an analog-to-digital converter, into the IMS-TOFMS system for the high-throughput analysis of highly complex proteolytic digests of, for example, blood plasma. To better address variable sample complexity, we have developed and rigorously evaluated a novel dynamic MP approach that ensures correlation of the analyzer performance with an ion source function and provides the improved dynamic range and sensitivity throughout the experiment. The MP IMS-TOFMS instrument has been shown to reliably detect peptides at a concentration of 1 nM in the presence of a highly complex matrix, as well as to provide a 3 orders of magnitude dynamic range and a mass measurement accuracy of better than 5 ppm. When matched against human blood plasma database, the detected IMS-TOF features were found to yield approximately 700 unique peptide identifications at a false discovery rate (FDR) of approximately 7.5%. Accounting for IMS information gave rise to a projected FDR of approximately 4%. Signal reproducibility was found to be greater than 80%, while the variations in the number of unique peptide identifications were <15%. A single sample analysis was completed in 15 min that constitutes almost 1 order of magnitude improvement compared to a more conventional LC-MS approach.     

Multiplexed ion mobility spectrometry-orthogonal time-of-flight mass spectrometry

Ion mobility spectrometry (IMS) coupled to orthogonal time-of-flight mass spectrometry (TOF) has shown significant promise for the characterization of complex biological mixtures. The enormous complexity of biological samples (e.g., from proteomics) and the need for both biological and technical analysis replicates imposes major challenges for multidimensional separation platforms with regard to both sensitivity and sample throughput. A major potential attraction of the IMS-TOF MS platform is separation speeds exceeding that of conventional condensed-phase separations by orders of magnitude. Known limitations of the IMS-TOF MS platforms that presently mitigate this attraction include the need for extensive signal averaging due to factors that include significant ion losses in the IMS-TOF interface and an ion utilization efficiency of less than approximately 1% with continuous ion sources (e.g., ESI). We have developed a new multiplexed ESI-IMS-TOF mass spectrometer that enables lossless ion transmission through the IMS-TOF as well as a utilization efficiency of >50% for ions from the ESI source. Initial results with a mixture of peptides show a approximately 10-fold increase in signal-to-noise ratio with the multiplexed approach compared to a signal averaging approach, with no reduction in either IMS or TOF MS resolution.     

Metabolomic analysis of eukaryotic tissue and prokaryotes using negative mode MALDI time-of-flight mass spectrometry

Metabolites in islets of Langerhans and Escherichia coli strain DH5-alpha were analyzed using negative-mode, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). For analysis of anionic metabolites by MALDI, 9-aminoacridine as the matrix yielded a far superior signal in comparison to alpha-cyano-4-hydroxycinnamic acid, 2,5-dihydrobenzoic acid, 2,4,6,-trihydroxyacetophenone, and 3-hydroxypicolinic acid. Limits of detection for metabolite standards were as low as 15 nM for GDP, GTP, ADP, and ATP and as high as 1 muM for succinate in 1-muL samples. Analysis of islet extracts allowed detection of 44 metabolites, 29 of which were tentatively identified by matching molecular weight to compounds in METLIN and KEGG databases. Relative quantification was demonstrated by comparing the ratio of selected di- and triphosphorylated nucleotides for islets incubated with different concentrations of glucose. For islets at 3 mM glucose, concentration ratios of ATP/ADP, GTP/GDP, and UTP/UDP were 1.9 +/- 1.39, 1.12 +/- 0.50, and 0.79 +/- 0.35 respectively, and at 20 mM glucose stimulation, the ratios increased to 4.13 +/- 1.89, 5.62 +/-4.48, and 4.30 +/- 4.07 (n = 3). Analysis was also performed by placing individual, intact islets on a MALDI target plate with matrix and impinging the laser directly on the dried islet. Direct analysis of single islets allowed detection of 43 metabolites, 28 of which were database identifiable. A total of 43% of detected metabolites from direct islet analysis were different from those detected in islet extracts. The method was extended to prokaryotic cells by analysis of extracts from E. coli. Sixty metabolites were detected, 39 of which matched compounds in the MetaCyc database. A total of 27% of the metabolites detected from prokaryotes overlapped those found in islets. These results show that MALDI can be used for detection of metabolites in complex biological samples.     

Detection of chemical weapon agents and simulants using chemical ionization reaction time-of-flight mass spectrometry

Chemical ionization reaction time-of-flight mass spectrometry (CIR-TOF-MS) has been used for the analysis of prepared mixtures of chemical weapon agents (CWAs) sarin and sulfur mustard. Detection of the CWA simulants 2-chloroethyl ethyl sulfide, triethyl phosphate, and dimethyl methyl phosphonate has also been investigated. Chemical ionization of all the agents and simulants was shown to be possible using the CIR-TOF-MS technique with a variety of reagent ions, and the sensitivity was optimized by variation of instrument parameters. The ionization process was found to be largely unaffected by sample humidity levels, demonstrating the potential suitability of the method to a range of environmental conditions, including the analysis of CWAs in air and in the breath of exposed individuals.     

Identification of arsenosugars at the picogram level using nanoelectrospray quadrupole time-of-flight mass spectrometry

State-of-the-art analytical methods for arsenic speciation rely typically on the availability of standards of defined structure, limiting the applicability of such methods to the determination of known compounds. Our previous high-energy tandem mass spectrometric studies demonstrated the strength of mass spectrometry for generating structurally diagnostic ions that allow for the identification of arsenic-containing ribofuranosides (arsenosugars) without the use of standards. We now report a more widely applicable and more sensitive approach, using negative-ion nano-electrospray low-energy tandem mass spectrometry for the generation of structurally useful product ions that allow for identification of arsenosugars at the picogram level. In the negative-ion mode, numerous product ions, suitable for characterizing naturally occurring dimethylated arsenosugars, were generated in high abundance. Application of the method to an algal extract unequivocally demonstrated the presence of a single dimethylated arsenosugar. In the positive-ion mode, characteristic tandem mass spectra were obtained for four trimethylarsonioribosides, allowing their identification without the need for standards. Overall it was demonstrated that nano-ES-MS/MS techniques can be used for characterizing arsenosugars on a routine basis, a necessary requirement for assessing potential health risks associated with consuming foods containing elevated levels of arsenosugars and for improving our understanding of arsenic biochemistry.     

Application of molecular beam deflection time-of-flight mass spectrometry to peptide analysis

The application of molecular beam deflection time-of-flight mass spectrometry (MBD-TOFMS) to peptide identification is described. The technique permits a simultaneous measurement of molecular mass and electric dipole susceptibility. The mass and susceptibility are not strongly correlated, and the results can be presented as a two-dimensional map. The susceptibility provides a useful way to disperse isobaric and isomeric peptides, and at least for small peptides, the susceptibility is significantly different for different amino acid sequences. Results for peptides in the mass range 1000-2300 Da show that the mass and susceptibility lead to a higher identification score than mass spectra alone.     

Development and evaluation of a glow discharge microwave-induced-plasma tandem source for time-of-flight mass spectrometry

In this work, a new glow discharge, microwave-induced-plasma (GDMIP), tandem ion source was developed, characterized, and used in conjunction with time-of-flight mass spectrometry. This tandem source was designed to be simple and compact The GD and the MIP unit are independent and demountable, providing flexibility in tuning and operating. The microwave plasma can be formed with very low power (a few watts) and overlapped with the glow discharge. The discharge current increased with the addition of microwave discharge when the GD was operated in constant-voltage mode, and the amplitude of the current increase was found to be related to microwave power, discharge pressure, and sampling distance. With the addition of microwave discharge, significant signal enhancement was achieved under a discharge pressure of 2.0 Torr and a discharge voltage of 500 V with 2.0-mm sampling distance. Enhanced factors of analyte signals ranging from approximately 1 to nearly 10 could be obtained with MIP boosting, while no significant change in noise level was observed. This new tandem source provides improved performance in direct solid sample analysis.     

Molecular depth profiling of multilayer polymer films using time-of-flight secondary ion mass spectrometry

The low penetration depth and high sputter rates obtained using polyatomic primary ions have facilitated their use for the molecular depth profiling of some spin-cast polymer films by secondary ion mass spectrometry (SIMS). In this study, dual-beam time-of-flight (TOF) SIMS (sputter ion, 5 keV SF(5)(+); analysis ion, 10 keV Ar(+)) was used to depth profile spin-cast multilayers of poly(methyl methacrylate) (PMMA), poly(2-hydroxyethyl methacrylate) (PHEMA), and trifluoroacetic anhydride-derivatized poly(2-hydroxyethyl methacrylate) (TFAA-PHEMA) on silicon substrates. Characteristic positive and negative secondary ions were monitored as a function of depth using SF(5)(+) primary ion doses necessary to sputter through the polymer layer and uncover the silicon substrate (>5 x10(14) ions/cm(2)). The sputter rates of the polymers in the multilayers were typically less than for corresponding single-layer films, and the order of the polymers in the multilayer affected the sputter rates of the polymers. Multilayer samples with PHEMA as the outermost layer resulted in lowered sputter rates for the underlying polymer layer due to increased ion-induced damage accumulation rates in PHEMA. Additionally, the presence of a PMMA or PHEMA overlayer significantly decreased the sputter rate of TFAA-PHEMA underlayers due to ion-induced damage accumulation in the overlayer. Typical interface widths between adjacent polymer layers were 10-15 nm for bilayer films and increased with depth to approximately 35 nm for the trilayer films. The increase in interface width and observations using optical microscopy showed the formation of sputter-induced surface roughness during the depth profiles of the trilayer polymer films. This study shows that polyatomic primary ions can be used for the molecular depth profiling of some multilayer polymer films and presents new opportunities for the analysis of thin organic films using TOF-SIMS.     

Postacquisition mass resolution improvement in time-of-flight secondary ion mass spectrometry

Good mass resolution can be difficult to achieve in time-of-flight secondary ion mass spectrometry (TOF-SIMS) when the analysis area is large or when the surface being analyzed is rough. In most cases, a significant improvement in mass resolution can be achieved by postacquisition processing of raw data. Methods are presented in which spectra are extracted from smaller regions within the original analysis area, recalibrated, and selectively summed to produce spectra with higher mass resolution than the original. No hardware modifications or specialized instrument tuning are required. The methods can be extended to convert the original raw file into a new raw file containing high mass resolution data. To our knowledge, this is the first report of conversion of a low mass resolution raw file into a high mass resolution raw file using only the data contained within the low mass resolution raw file. These methods are applicable to any material but are expected to be particularly useful in analysis of difficult samples such as fibers, powders, and freeze-dried biological specimens.