High Mass Measurement Accuracy Research Articles

Identification of leptomeningeal metastasis‐related proteins in cerebrospinal fluid of patients with breast cancer by a combination of MALDI‐TOF, MALDI‐FTICR and nanoLC‐FTICR MS

Leptomeningeal metastasis (LM) is a devastating complication occurring in 5% of breast cancer patients. However, the current 'gold standard' of diagnosis, namely microscopic examination of the cerebrospinal fluid (CSF), is false-negative in 25% of patients at the first lumbar puncture. In a previous study, we analyzed a set of 151 CSF samples (tryptic digests) by MALDI-TOF and detected peptide masses that were differentially expressed in breast cancer patients with LM. In the present study, we obtain for a limited number of samples exact masses for these peptides by MALDI-FTICR MS measurements. Identification of these peptides was performed by electrospray FTICR MS after separation by nano-scale LC. The database results were confirmed by targeted high mass accuracy measurements of the fragment ions in the FTICR cell. The combination of automated high-throughput MALDI-TOF measurements and analysis by FTICR MS leads to the identification of 17 peptides corresponding to 9 proteins. These include proteins that are operative in host-disease interaction, inflammation and immune defense (serotransferrin, alpha 1-antichymotrypsin, hemopexin, haptoglobin and transthyretin). Several of these proteins have been mentioned in the literature in relation to cancer. The identified proteins alpha1-antichymotrypsin and apolipoprotein E have been described in relation to Alzheimer's disease and brain cancer.

Proteome Profile of Cytosolic Component of Zebrafish Liver Generated by LC−ESI MS/MS Combined with Trypsin Digestion and Microwave-Assisted Acid Hydrolysis

The zebrafish genome has recently been sequenced and annotated allowing for high-throughput proteomic analysis. Here, we report for the first time a proteomic subset of zebrafish liver, an important organ for metabolizing toxins. Using a newly developed analytical procedure, we have identified 1204 proteins from the cytosolic component of a zebrafish liver tissue sample. Our methods involve cell-compartment fractionation of liver tissue samples, four levels of protein digestion, and off-line two-dimensional liquid chromatography (2-D LC) separations of resultant peptides. Proteins are identified using an electrospray ionization quadrupole time-of-flight tandem mass spectrometer (ESI-QTOF MS/MS), which provides high-resolution and high-accuracy mass measurement of peptide ions and their fragment ions. We demonstrate that greater proteome coverage can be achieved by combining the results obtained from four methods of protein digestion: three tryptic digests (one in buffer, one in methanol, and another in SDS), and a microwave-assisted acid hydrolysate of the protein extracts. Identified proteins--which included several groups of established protein biomarkers--were functionally classified. We discuss the functions and implications of these biomarkers within the context of zebrafish toxicology.

Collision-Induced Dissociative Chemical Cross-Linking Reagents and Methodology: Applications to Protein Structural Characterization Using Tandem Mass Spectrometry Analysis

Chemical cross-linking combined with mass spectrometry is a viable approach to study the low-resolution structure of protein and protein complexes. However, unambiguous identification of the residues involved in a cross-link remains analytically challenging. To enable a more effective analysis across various MS platforms, we have developed a novel set of collision-induced dissociative cross-linking reagents and methodology for chemical cross-linking experiments using tandem mass spectrometry (CID-CXL-MS/MS). These reagents incorporate a single gas-phase cleavable bond within their linker region that can be selectively fragmented within the in-source region of the mass spectrometer, enabling independent MS/MS analysis for each peptide. Initial design concepts were characterized using a synthesized cross-linked peptide complex. Following verification and subsequent optimization of cross-linked peptide complex dissociation, our reagents were applied to homodimeric glutathione S-transferase and monomeric bovine serum albumin. Cross-linked residues identified by our CID-CXL-MS/MS method were in agreement with published crystal structures and previous cross-linking studies using conventional approaches. Common LC/MS/MS acquisition approaches such as data-dependent acquisition experiments using ion trap mass spectrometers and product ion spectral analysis using SEQUEST were shown to be compatible with our CID-CXL-MS/MS reagents, obviating the requirement for high resolution and high mass accuracy measurements to identify both intra- and interpeptide cross-links.

PEPPeR, a Platform for Experimental Proteomic Pattern Recognition

Quantitative proteomics holds considerable promise for elucidation of basic biology and for clinical biomarker discovery. However, it has been difficult to fulfill this promise due to over-reliance on identification-based quantitative methods and problems associated with chromatographic separation reproducibility. Here we describe new algorithms termed "Landmark Matching" and "Peak Matching" that greatly reduce these problems. Landmark Matching performs time base-independent propagation of peptide identities onto accurate mass LC-MS features in a way that leverages historical data derived from disparate data acquisition strategies. Peak Matching builds upon Landmark Matching by recognizing identical molecular species across multiple LC-MS experiments in an identity-independent fashion by clustering. We have bundled these algorithms together with other algorithms, data acquisition strategies, and experimental designs to create a Platform for Experimental Proteomic Pattern Recognition (PEPPeR). These developments enable use of established statistical tools previously limited to microarray analysis for treatment of proteomics data. We demonstrate that the proposed platform can be calibrated across 2.5 orders of magnitude and can perform robust quantification of ratios in both simple and complex mixtures with good precision and error characteristics across multiple sample preparations. We also demonstrate de novo marker discovery based on statistical significance of unidentified accurate mass components that changed between two mixtures. These markers were subsequently identified by accurate mass-driven MS/MS acquisition and demonstrated to be contaminant proteins associated with known proteins whose concentrations were designed to change between the two mixtures. These results have provided a real world validation of the platform for marker discovery.

High-accuracy mass measurements of neutron-rich Kr isotopes

The atomic masses of the neutron-rich krypton isotopes {sup 84,86-95}Kr have been determined with the tandem Penning trap mass spectrometer ISOLTRAP with uncertainties ranging from 20 to 220 ppb. The masses of the short-lived isotopes {sup 94}Kr and {sup 95}Kr were measured for the first time. The masses of the radioactive nuclides {sup 89}Kr and {sup 91}Kr disagree by 4 and 6 standard deviations, respectively, from the present Atomic-Mass Evaluation database. The resulting modification of the mass surface with respect to the two-neutron separation energies as well as implications for mass models and stellar nucleosynthesis are discussed.

Sub Parts-Per-Million Mass Measurement Accuracy of Intact Proteins and Product Ions Achieved Using a Dual Electrospray Ionization Quadrupole Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

High mass measurement accuracy (MMA) is demonstrated for intact proteins and subsequent collision-induced dissociation product ions using internal calibration. Internal calibration was accomplished using a dual electrospray ionization source coupled with a hybrid quadrupole Fourier transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer. Initially, analyte ions generated via the first electrospray (ESI) emitter are isolated and dissociated in the external quadrupole. This event is followed by a simultaneous switch to the calibrant ion ESI emitter and a disablement of the isolation and activation of the external quadrupole such that a broad m/z range of calibrant ions are accumulated before injecting the analyte/calibrant ion mixture into the ICR cell. Two different internal calibrant solutions were utilized in these studies to evaluate this approach for the top-down characterization of melittin and ubiquitin. While external calibration of protein fragments resulted in absolute MMA greater than 16 ppm, internal standardization significantly improved upon the MMA of both the intact proteins and their products ions which ranged from -2.0 ppm to 1.1 ppm, with an average of -0.9 ppm. This method requires limited modification to ESI-FT-ICR mass spectrometers and is applicable for both positive and negative ionization modes.

Oxodicarboxylic acids in atmospheric aerosol particles

Fine mode aerosol was collected on quartz fiber filters at several sites across Europe. These samples were analyzed for carboxylic acids by liquid chromatography coupled to a hybrid (quadrupole and time-of-flight) mass spectrometer (LC/MS/MS-TOF). A series of oxodicarboxylic acids (C 7–C 11) was detected. Oxodicarboxylic acids are linear dicarboxylic acids with an additional carbonyl group. Previous measurements of these acids are scarce and their sources are largely unknown. Several structural isomers (different positions of the carbonyl group within the molecule) could be identified and differentiated by the combination of laboratory experiments and high mass accuracy measurements. The homologs with 9–11 carbon atoms were identified for the first time in atmospheric aerosol particles. The concentrations of oxodicarboxylic acids in ambient aerosol samples frequently exceeded those of the corresponding unsubstituted dicarboxylic acids. Oxodicarboxylic acids have been shown to be products of the reaction of dicarboxylic acids with OH radicals in chamber experiments and a reaction mechanism is proposed. Good correlation of oxodicarboxylic acid and hydroxyl radical concentrations was found at two measurement sites (Finland and Crete) of different geographic location and meteorological conditions. The ratios of individual isomers from the field samples are comparable to those of the laboratory experiments. The results of this study imply that the reaction of OH radicals and dicarboxylic acids is an important pathway for the production of oxodicarboxylic acids in the atmosphere. Oxodicarboxylic acids seem to be important intermediates in atmospheric oxidation processes of organic compounds.

New Mass Value forLi7

A high-accuracy mass measurement of $^{7}\mathrm{Li}$ was performed with the SMILETRAP Penning-trap mass spectrometer via a cyclotron frequency comparison of $^{7}\mathrm{Li}^{3+}$ and $\mathrm{H}_{2}{}^{+}$. A new atomic-mass value of $^{7}\mathrm{Li}$ has been determined to be $7.016\text{ }003\text{ }425\text{ }6(45)\text{ }\text{ }\mathrm{u}$ with a relative uncertainty of 0.63 ppb. It has uncovered a discrepancy as large as $14\ensuremath{\sigma}$ ($1.1\text{ }\text{ }\ensuremath{\mu}\mathrm{u}$) deviation relative to the literature value given in the Atomic-Mass Evaluation AME 2003. The importance of the improved and revised $^{7}\mathrm{Li}$ mass value, for calibration purposes in nuclear-charge radii and atomic-mass measurements of the neutron halos $^{9}\mathrm{Li}$ and $^{11}\mathrm{Li}$, is discussed.

Performance Evaluation of a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer

Design and performance of a novel hybrid mass spectrometer is described. It couples a linear ion trap mass spectrometer to an orbitrap mass analyzer via an rf-only trapping quadrupole with a curved axis. The latter injects pulsed ion beams into a rapidly changing electric field in the orbitrap wherein they are trapped at high kinetic energies around an inner electrode. Image current detection is subsequently performed after a stable electrostatic field is achieved. Fourier transformation of the acquired transient allows wide mass range detection with high resolving power, mass accuracy, and dynamic range. The entire instrument operates in LC/MS mode (1 spectrum/s) with nominal mass resolving power of 60,000 and uses automatic gain control to provide high-accuracy mass measurements, within 2 ppm using internal standards and within 5 ppm with external calibration. The maximum resolving power exceeds 100,000 (fwhm). Rapid, automated data-dependent capabilities enable real-time acquisition of up to three high-mass accuracy MS/MS spectra per second.

Making Broad Proteome Protein Measurements in 1−5 min Using High-Speed RPLC Separations and High-Accuracy Mass Measurements

The throughput of proteomics measurements that provide broad protein coverage is limited by the quality and speed of both the separations as well as the subsequent mass spectrometric analysis; at present, analysis times can range anywhere from hours (high throughput) to days or longer (low throughput). We have explored the basis for proteomics analyses conducted on the order of minutes using high-speed capillary RPLC combined through on-line electrospray ionization interface with high-accuracy mass spectrometry (MS) measurements. Short 0.8-microm porous C18 particle-packed 50-microm-i.d. capillaries were used to speed the RPLC separations while still providing high-quality separations. Both time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FTICR) MS were applied for identifying peptides using the accurate mass and time (AMT) tag approach. Peptide RPLC relative retention (elution) times that were generated by solvent gradients that differed by at least 25-fold were found to provide relative elution times that agreed to within 5%, which provides the basis for using peptide AMT tags for higher throughput proteomics measurements. For fast MS acquisition speeds (e.g., 0.2 s for TOF and either approximately 0.3 or approximately 0.6 s for FTICR), peptide mass measurement accuracies of better than +/-15 ppm were obtained with the high-speed RPLC separations. The ability to identify peptides and the overall proteome coverage was determined by factors that include the separation peak capacity, the sensitivity of the MS (with fast scanning), and the accuracy of both the mass measurements and the relative RPLC peptide elution times. The experimental RPLC relative elution time accuracies of 5% (using high-speed capillary RPLC) and mass measurement accuracies of better than +/-15 ppm allowed for the confident identification of >2800 peptides and >760 proteins from >13,000 different putative peptides detected from a Shewanellaoneidensis tryptic digest. Initial results for both RPLC-ESI-TOF and RPLC-ESI-FTICR MS were similar, with approximately 2000 different peptides from approximately 600 different proteins identified within 2-3 min. For <120-s proteomic analysis, TOF MS analyses were more effective, while FTICR MS was more effective for the >150-s analysis due to the improved mass accuracies attained using longer spectrum acquisition times.

Weighing excited nuclear states with a Penning trap mass spectrometer

We report on high-accuracy mass measurements and isomer identification of 187Pb. In this nuclide, two close-lying isomeric states are known from α-decay studies. With the combined use of the ISOLDE resonance ionization laser ion source and the Penning trap mass spectrometer ISOLTRAP the energy difference of 187Pb and 187 m Pb was determined to be E = 33 ( 13 ) keV . This is the lowest isomeric excitation energy ever determined by weighing nuclei.

Increased Protein Identification Capabilities through Novel Tandem MS Calibration Strategies

High mass measurement accuracy is critical for confident protein identification and characterization in proteomics research. Fourier transform ion cyclotron resonance (FTICR) mass spectrometry is a unique technique which can provide unparalleled mass accuracy and resolving power. However, the mass measurement accuracy of FTICR-MS can be affected by space charge effects. Here, we present a novel internal calibrant-free calibration method that corrects for space charge-induced frequency shifts in FTICR fragment spectra called Calibration Optimization on Fragment Ions (COFI). This new strategy utilizes the information from fixed mass differences between two neighboring peptide fragment ions (such as y(1) and y(2)) to correct the frequency shift after data collection. COFI has been successfully applied to LC-FTICR fragmentation data. Mascot MS/MS ion search data demonstrate that most of the fragments from BSA tryptic digested peptides can be identified using a much lower mass tolerance window after applying COFI to LC-FTICR-MS/MS of BSA tryptic digest. Furthermore, COFI has been used for multiplexed LC-CID-FTICR-MS which is an attractive technique because of its increased duty cycle and dynamic range. After the application of COFI to a multiplexed LC-CID-FTICR-MS of BSA tryptic digest, we achieved an average measured mass accuracy of 2.49 ppm for all the identified BSA fragments.

Advanced Oxidation of Caffeine in Water: On-Line and Real-Time Monitoring by Electrospray Ionization Mass Spectrometry

High performance liquid chromatography (HPLC), ultraviolet spectroscopy (UV), and total organic carbon (TOC) analyses show that caffeine is quickly and completely degraded underthe oxidative conditions of the UV/H2O2,TiO2/ UV, and Fenton systems but that the organic carbon content of the solution decreases much more slowly. Continuous on-line and real-time monitoring by electrospray ionization mass (ESI-MS) and tandem mass spectrometric experiments (ESI-MS/MS) as well as high accuracy MS measurements and gas chromatography-mass spectrometry analysis show that caffeine is first oxidized to N-dimethylparabanic acid likely via initial OH insertion to the C4=C8 caffeine double bond. A second degradation intermediate, di(N-hidroxymethyl)parabanic acid, has been identified by ESI-MS and characterized by ESI-MS/MS and high accuracy mass measurements. This polar and likely relatively unstable compound, which is not detected by off-line GC-MS analysis, is likely formed via further oxidation of N-dimethylparabanic acid at both of its N-methyl groups and constitutes an unprecedented intermediate in the degradation of caffeine.

The LEBIT 9.4 T Penning trap system

The initial experimental program with the Low-Energy Beam and Ion Trap Facility, or LEBIT, will concentrate on Penning trap mass measurements of rare isotopes, delivered by the Coupled Cyclotron Facility (CCF) of the NSCL. The LEBIT Penning trap system has been optimized for high-accuracy mass measurements of very short-lived isotopes.

Automated accurate mass data processing using a gas chromatograph/time‐of‐flight mass spectrometer in drug discovery

A gas chromatograph/time-of-flight (GCT) mass spectrometer, with high mass measurement accuracy to within 5 ppm, has been used for the automated accurate mass analysis of multicomponent mixtures and drug discovery compounds. A multicomponent mixture was analyzed several times over the course of a week to assess the reproducibility and ruggedness of the automated method while operating the GCT in electron ionization mode. For example, the data for 31 radical cations generated via electron ionization was processed using automated software (i.e. OpenLynx) to provide for mass accuracies less than 5 ppm for nearly 100% of the ions from multiple injection data. Mass accuracies of the radical anions of polyaromatic hydrocarbons generated via negative chemical ionization, and protonated pyridines and quinolines generated via methane chemical ionization, were mainly less than 5 ppm from multiple injection data. In addition, the automated method has been used for the accurate mass analysis of drug discovery compounds.

Statistical Evaluation of Internal and External Mass Calibration Laws Utilized in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

The statistical evaluation of two common and three new calibration laws utilized in Fourier transform ion cyclotron resonance mass spectrometry are presented. Electrospray ionization was used to prepare a series of mass spectra of ammonium-adducted polypropylene glycol (PPG) with an average molecular weight of 1000 Da. The singly charged PPG-1000 oligomers allowed for the description of a broad range of m/z and abundance values within each mass spectrum. The hexapole accumulation time was varied to afford a range of total ion abundance values of about an order of magnitude. To examine each of the calibration laws, we utilized cross-validation both "within-spectrum" and "between-spectra" for internally and externally calibrated data, respectively. In addition, we used t-statistics to ensure that each calibration coefficient was statistically significant and necessary to accurately describe the variation in the data. In comparison to commonly used calibration laws for internal calibration, our new calibration law based on multiple linear regression offered a 2-fold improvement in mass measurement accuracy (MMA). In comparison to external calibration laws without automatic gain control, our new calibration law using multiple regression improved the MMA by >10-fold; this improvement would increase further as the dynamic range of the measurement increases (e.g., a biological system). For both our internal and external calibration laws, the median MMA was less than 1 part-per-million. Furthermore, we investigate the number of calibrant ions as well as their required m/z range in order to successfully achieve high MMA.

Effect of post‐excitation radius on ion abundance, mass measurement accuracy, and isotopic distributions in Fourier transform ion cyclotron resonance mass spectrometry

We report an evaluation of a modern Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) instrument to determine the general trend of post-excitation radius on total ion abundance, mass measurement accuracy, and isotopic distributions for internally calibrated mass spectra. The optimum post-excitation radius was determined using total ion abundance, mass measurement accuracy (MMA), and isotope ratios. However, despite the utility of internal calibration for achieving ultimate MMA, the internal calibrant ions were insufficient for compensating for sub-optimum ICR cell conditions. The findings presented herein underscore the importance of determining the optimal post-excitation radius in FT-ICR-MS to achieve high ion abundance (low limits of detection), high MMA, and valid isotopic distributions.

Instrumentation and Method for Ultrahigh Resolution Field Desorption Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Nonpolar Species

We describe the construction and application of a 9.4-T FT-ICR mass spectrometer interfaced to a commercial field desorption ion source for high-resolution, high-mass accuracy measurements of nonpolar species. The FT-ICR MS instrument includes a liquid injection field desorption ionization source, octopole ion guides, external octopole ion trap capable of an axial potential gradient for ion ejection, capacitively coupled open cylindrical ion trap, and pulsed gas valve for ion cooling. Model compound responses with regard to various source and instrument conditions provide a basis for interpretation of broadband mass spectra of complex mixtures. As an example, we demonstrate broadband speciation of a Gulf Coast crude oil, with respect to numerous heteroatomic classes, compound types (rings plus double bonds), and carbon number distributions.

Improved mass accuracy for tandem mass spectrometry

With the emergence of top-down proteomics, the ability to achieve high mass measurement accuracy on tandem MS/MS data will be beneficial for protein identification and characterization. (FT-ICR) Fourier transform ion cyclotron resonance mass spectrometers are the ideal instruments to perform these experiments with their ability to provide high resolution and mass accuracy. A major limitation to mass measurement accuracy in FT-ICR instruments arises from the occurrence of space charge effects. These space charge effects shift the cyclotron frequency of the ions, which compromises the mass measurement accuracy. While several methods have been developed that correct these space charge effects, they have limitations when applied to MS/MS experiments. It has already been shown that additional information inherent in electrospray spectra can be used for improved mass measurement accuracy with the use of a computer algorithm called DeCAL (deconvolution of Coulombic affected linearity). This paper highlights a new application of the strategy for improved mass accuracy in tandem mass analysis. The results show a significant improvement in mass measurement accuracy on complex electron capture dissociation spectra of proteins. We also demonstrate how the improvement in mass accuracy can increase the confidence in protein identification from the fragment masses of proteins acquired in MS/MS experiments.

Towards precision experiments with LEBIT at NSCL/MSU

The Low Energy Beam and Ion Trap (LEBIT) Project is getting closer to its goal to convert the high-energy fragment beams produced at NSCL/MSU into low-energy low-emittance beams. This beam manipulation will be done by a combination of a high-pressure gas stopping cell and a radiofrequency quadrupole (RFQ) ion accumulator and buncher. The first experimental program to benefit from the low-energy beams produced will be high-accuracy mass measurements on very short-lived isotopes with a 9.4 T Penning trap system. The status of the project is presented with an emphasis on LEBIT's advanced trapping techniques.