Chemical Noise Research Articles

Direct Determination of Urinary Creatinine by Reactive-Thermal Desorption-Extractive Electrospray-Ion Mobility-Tandem Mass Spectrometry.

A direct, ambient ionization method has been developed for the determination of creatinine in urine that combines derivatization and thermal desorption with extractive electrospray ionization and ion mobility-mass spectrometry. The volatility of creatinine was enhanced by a rapid on-probe aqueous acylation reaction, using a custom-made thermal desorption probe, allowing thermal desorption and ionization of the monoacylated derivative. The monoacyl creatinine [M + H]+ ion (m/z 156) was subjected to mass-to-charge selection and collision induced dissociation to remove the acyl group, generating the protonated creatinine [M + H]+ product ion at m/z 114 before an ion mobility separation was applied to reduce chemical noise. Stable isotope dilution using creatinine-d3 as internal standard was used for quantitative measurements. The direct on-probe derivatization allows high sample throughput with a typical cycle time of 1 min per sample. The method shows good linearity (R2 = 0.986) and repeatability (%RSD 8–10%) in the range of 0.25–2.0 mg/mL. The creatinine concentrations in diluted urine samples from a healthy individual were determined to contain a mean concentration of 1.44 mg/mL creatinine with a precision (%RSD) of 9.9%. The reactive ambient ionization approach demonstrated here has potential for the determination of involatile analytes in urine and other biofluids.

Transmission Mode Desorption Electrospray Ionization (TM-DESI) for Simultaneous Analysis of Potential Inorganic and Organic Components of Radiological Dispersion Devices (RDDs)

Transmission mode desorption electrospray ionization (TM-DESI) coupled to an ion trap mass spectrometer capable of source collision-induced dissociation (CID) was used to completely analyze radiological dispersion device components. Source CID significantly enhanced the signal for metal ions by reducing adducts while eliminating chemical noise from background molecules through extensive fragmentation. Source CID spectra yielded reasonably accurate isotopic ratios for the metals studied. By switching the source CID on and off between scans, all major constituents in mixtures of simulated radionuclides and explosives were simultaneously observed. These results indicate that TM-DESI/ion trap technology could be a powerful on-site tool for nuclear forensics.

1,8-Bis(dimethylamino)naphthalene/9-aminoacridine: A new binary matrix for lipid fingerprinting of intact bacteria by matrix assisted laser desorption ionization mass spectrometry

The effectiveness of a novel binary matrix composed of 1,8-bis(dimethylamino)naphthalene (DMAN; proton sponge) and 9-aminoacridine (9AA) for the direct lipid analysis of whole bacterial cells by matrix assisted laser desorption ionization mass spectrometry (MALDI MS) is demonstrated. Deprotonated analyte signals nearly free of matrix-related ions were observed in negative ion mode. The effect of the most important factors (laser energy, pulse voltage, DMAN/9AA ratio, analyte/matrix ratio) was investigated using a Box–Behnken response surface design followed by multi-response optimization in order to simultaneously maximize signal-to-noise (S/N) ratio and resolution. The chemical surface composition of single or mixed matrices was explored by X-ray photoelectron spectroscopy (XPS). Moreover, XPS imaging was used to map the spatial distribution of a model phospholipid in single or binary matrices.The DMAN/9AA binary matrix was then successfully applied to the analysis of intact Gram positive (Lactobacillus sanfranciscensis) or Gram negative (Escherichia coli) microorganisms. About fifty major membrane components (free fatty acids, mono-, di- and tri-glycerides, phospholipids, glycolipids and cardiolipins) were quickly and easily detected over a mass range spanning from ca. 200 to ca. 1600m/z. Moreover, mass spectra with improved S/N ratio (compared to single matrices), reduced chemical noise and no formation of matrix-clusters were invariably obtained demonstrating the potential of this binary matrix to improve sensitivity.

Characterization of PM10 in the ambient air during Deepawali festival of Rajnandgaon district, India

Deepawali is one of the main festivals for Hindu religion which falls in the period October–November every year with great fireworks display. In this study, we investigated the levels of water soluble ions and heavy metals—during the fireworks festival in Rajnandgaon, Central India. The chemical compositions and noise level distributions are reported from the sampling site. First time during Deepawali, air quality was studied in this area, The Aerosol samples of PM10 (particle aerodynamic diameter <10 μm) are collected in October 24–28, 2011. Aims of the present studies are (1) To describe the particulate concentrations and associated chemical species during Deepawali festival, (2) To recognize the noise level in Deepawali festival. For study, the samples were collected in glass fiber filter paper and analyzed for the major water soluble ions F−, Cl−, NO3 −, SO4 2−, Na2+, NH4 +, K+, Ca2+, and Mg2+ employing ion chromatograph. Concentration of heavy metals was analyzed by ICP-MS and was observed to occur in order Fe > Zn > Pb > Ni > Cr > Cd. The result revels that all concentration are above the permissible limit fixed by CPCB, USPEA, and WHO standard. It is concluded that the burning of fireworks during Deepawali festival was the main source of heavy metals and ion.

Preanalytical Aspects and Sample Quality Assessment in Metabolomics Studies of Human Blood

Metabolomics is a powerful tool that is increasingly used in clinical research. Although excellent sample quality is essential, it can easily be compromised by undetected preanalytical errors. We set out to identify critical preanalytical steps and biomarkers that reflect preanalytical inaccuracies. We systematically investigated the effects of preanalytical variables (blood collection tubes, hemolysis, temperature and time before further processing, and number of freeze-thaw cycles) on metabolomics studies of clinical blood and plasma samples using a nontargeted LC-MS approach. Serum and heparinate blood collection tubes led to chemical noise in the mass spectra. Distinct, significant changes of 64 features in the EDTA-plasma metabolome were detected when blood was exposed to room temperature for 2, 4, 8, and 24 h. The resulting pattern was characterized by increases in hypoxanthine and sphingosine 1-phosphate (800% and 380%, respectively, at 2 h). In contrast, the plasma metabolome was stable for up to 4 h when EDTA blood samples were immediately placed in iced water. Hemolysis also caused numerous changes in the metabolic profile. Unexpectedly, up to 4 freeze-thaw cycles only slightly changed the EDTA-plasma metabolome, but increased the individual variability. Nontargeted metabolomics investigations led to the following recommendations for the preanalytical phase: test the blood collection tubes, avoid hemolysis, place whole blood immediately in ice water, use EDTA plasma, and preferably use nonrefrozen biobank samples. To exclude outliers due to preanalytical errors, inspect the biomarker signal intensities reflecting systematic as well as accidental and preanalytical inaccuracies before processing the bioinformatics data.

DMS-MS separations with different transport gas modifiers

The current trend in analytical measurements is towards a new generation of mass spectrometry (MS) systems with enhanced sensitivity and high throughput of measurements. At the same time, increasing the sensitivity of MS can augment potential problems with isobaric interferences, which can reveal the undesirable effect of chemical noise on quality of analysis, particularly for quantitative measurements. Therefore, fast and effective methods of sample pretreatment which help to reduce the sample complexity are needed. Over the past decade it has been established that differential mobility spectrometry (DMS) can be employed as an effective pre-separation technique for atmospheric pressure ionization MS. DMS ion pre-filtering can improve simultaneously two vital parameters for mass spectrometry; signal to noise ratio and selectivity of MS measurement. In addition it was found that adding the appropriate amount of chemical modifiers to the transport gas can substantially enhance the resolving power of DMS. This valuable finding was immediately accepted and currently is exploited in commercial DMS-MS systems. The goal of this paper is to expand the understanding and systematization of the current knowledge related to augmentation of the separation power of DMS by adding chemical modifiers into the gas stream. This manuscript, reports systematic experimental data for a 140 chemicals mixture, measured within a DMS cell in the presence and absence of chemical modifiers. These data help to map out the behavior of chemical entities for different compositions of transport gases, including nitrogen, nitrogen/helium mixtures, and nitrogen with the addition of various polar and non-polar modifiers.

Chemical Noise Produced by Equilibrium Adsorption/Desorption of Surface Pyridine at Au–Ag–Au Bimetallic Atom-Scale Junctions Studied by Fluctuation Spectroscopy

The chemical noise contained in conductance fluctuations resulting from adsorption and desorption of pyridine at Au-Ag-Au bimetallic atom-scale junctions (ASJs) exhibiting ballistic electron transport is studied using fluctuation spectroscopy. ASJs are fabricated by electrochemical Ag deposition in a Au nanogap to produce a high-conductance Ag quantum wire, followed by electromigration-induced thinning in pyridine solution to create stable ASJs. The conductance behavior of the resulting ASJs is analyzed by sequential autocorrelation and Fourier transform of the current-time data to yield the power spectral density (PSD). In these experiments the PSDs from Ag ASJs in pyridine exhibit two main frequency regions: 1/f noise originating from resistance fluctuations of the junction itself at low frequencies, and a Lorentzian noise component arising from molecular adsorption/desorption fluctuations at higher frequencies. The characteristic cutoff frequency of the Lorentzian noise component determines the relaxation time of molecular fluctuations, which, in turn, is sensitive to the kinetics of the adsorption/desorption process. The kinetics are found to depend on concentration and on the adsorption binding energy. The junction size (<5G0), on the other hand, does not affect the kinetics, as the cutoff frequency remains unchanged. Concentration-dependent adsorption free energies are interpreted as arising from a distribution of binding energies, N(E(b)), on the Ag ASJ. Other observations, such as long lifetime ASJs and two-level fluctuations in conductance, provide additional evidence for the integral role of the adsorbate in determining ASJ reorganization dynamics.

Fluctuations in Tat copy number when it counts the most: a possible mechanism to battle the HIV latency

The HIV-1 virus can enter a dormant state and become inactive, which reduces accessibility by antiviral drugs. We approach this latency problem from an unconventional point of view, with the focus on understanding how intrinsic chemical noise (copy number fluctuations of the Tat protein) can be used to assist the activation process of the latent virus. Several phase diagrams have been constructed in order to visualize in which regions of the parameter space noise can drive the activation process. Essential to the study is the use of a hyperbolic coordinate system, which greatly facilitates quantification of how the various reaction rate combinations shape the noise behavior of the Tat protein feedback system. We have designed a mathematical manual of how to approach the problem of activation quantitatively, and introduce the notion of an “operating point” of the virus. For both noise-free and noise-based strategies we show how operating point off-sets induce changes in the number of Tat molecules. The major result of the analysis is that for every noise-free strategy there is a noise-based strategy that requires lower dosage, but achieves the same anti-latency effect. It appears that the noise-based activation is advantageous for every operating point.

Matrix Assisted Ionization Vacuum (MAIV), a New Ionization Method for Biological Materials Analysis Using Mass Spectrometry

The introduction of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) for the mass spectrometric analysis of peptides and proteins had a dramatic impact on biological science. We now report that a wide variety of compounds, including peptides, proteins, and protein complexes, are transported directly from a solid-state small molecule matrix to gas-phase ions when placed into the vacuum of a mass spectrometer without the use of high voltage, a laser, or added heat. This ionization process produces ions having charge states similar to ESI, making the method applicable for high performance mass spectrometers designed for atmospheric pressure ionization. We demonstrate highly sensitive ionization using intermediate pressure MALDI and modified ESI sources. This matrix and vacuum assisted soft ionization method is suitable for the direct surface analysis of biological materials, including tissue, via mass spectrometry.

An Ion Mobility Assisted Data Independent LC-MS Strategy for the Analysis of Complex Biological Samples

The use of gas-phase ion mobility separation in LC-MS based bottom-up proteomic experiments is described. A data-independent acquisition approach was employed in combination with one and two dimensional reversed phase liquid chromatography separations. The ion mobility component in the acquisition schema affords additional acquisition specificity and improved peptide resolution in terms of system peak capacity. The additional acquisition specificity was mainly achieved by means of the combined retention and drift time association of product to precursor ions and chemical noise reduction. Experimental data from replicate experiments were utilized to determine the rate of increase for the number of detected ions and deconvoluted accurate mass – retention time pairs and protein and peptide identifications as a measure of peak capacity by varying mass spectral resolution, consideration of multidimensional separations and the incorporation of ion mobility into the analytical schema. The presented data reveals a high degree of reproducibility at the ion detection, peptide and protein level, when analyzed under identical conditions, with a concurrent average increase in the number of identified peptides and proteins of 160% in the instance of mobility assisted acquisitions. Two-dimensional separations independently improved the peptide and protein identification rates by another 260% and 320%, respectively. Collectively, both separation techniques, reversed phase chromatography and ion mobility, increased the peak capacity and number of peptides and proteins significantly. The applicability of the technique and instrument platform for qualitative and quantitative proteomics studies will be demonstrated.

Enhanced performance in the determination of ibuprofen 1-β-O-acyl glucuronide in urine by combining high field asymmetric waveform ion mobility spectrometry with liquid chromatography-time-of-flight mass spectrometry

The incorporation of a chip-based high field asymmetric waveform ion mobility spectrometry (FAIMS) separation in the ultra (high)-performance liquid chromatography–high resolution mass spectrometry (UHPLC–HRMS) determination of the (R/S) ibuprofen 1-β-O-acyl glucuronide metabolite in urine is reported. UHPLC–FAIMS–HRMS reduced matrix chemical noise, improved the limit of quantitation approximately two-fold and increased the linear dynamic range compared to the determination of the metabolite without FAIMS separation. A quantitative evaluation of the prototype UHPLC–FAIMS–HRMS system showed better reproducibility for the drug metabolite (%RSD 2.7%) at biologically relevant concentrations in urine. In-source collision induced dissociation of the FAIMS-selected deprotonated metabolite was used to fragment the ion prior to mass analysis, enhancing selectivity by removing co-eluting species and aiding the qualitative identification of the metabolite by increasing the signal-to-noise ratio of the fragment ions.

Finding the REAL differences among biochemical and chemical noise in Metabolomics profiling experiments

Finding the REAL differences among biochemical and chemical noise in Metabolomics profiling experiments

LC-MS/MS quantification of salvinorin A from biological fluids

A facile method for quantifying the concentration of the powerful and widely available hallucinogen salvinorin A (a selective kappa opioid agonist) from non-human primate cerebrospinal fluid (CSF) and human plasma has been developed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in positive electrospray ionization (ESI) mode. With CSF solid phase extraction can be avoided completely by simply diluting each sample to 10 % (v/v) acetonitrile, 1 % (v/v) formic acid and injecting under high aqueous conditions for analyte focusing. Extensive plasma sample preparation was investigated including protein precipitation, SPE column selection, and plasma particulate removal. Human plasma samples were centrifuged at 21,000 × gravity for 4 minutes to obtain clear particulate-free plasma, from which 300 μl was spiked with internal standard and loaded onto a C18 SPE column with a 100 mg mL-1 loading capacity. Guard columns (C18, hand packed 1 mm × 20 mm) were exchanged after backpressure increased above 4600psi, about 250 injections. A shallow acetonitrile/water gradient was used, 29 to 33% CH3CN over 8 minutes to elute salvinorin A. Reduction of chemical noise was achieved using tandem mass spectrometry with multiple reaction monitoring while sensitivity increases were observed using a 50 μL injection volume onto a small bore analytical column (C18, 1 mm ID × 50 mm) thus increasing peak concentration. Limits of quantification were found to be 0.0125 ng mL-1 (CSF) and 0.05 ng mL-1 (plasma) with interday precision and accuracy below 1.7 % and 9.42 % (CSF) and 3.47 % and 12.37 % (plasma) respectively. This method was used to determine the concentration of salvinorin A from an in vivo Rhesus monkey study and a trial of healthy human research participants, using behaviorally active doses.

High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics

High-field asymmetric waveform ion mobility spectrometry (FAIMS) is an atmospheric pressure ion mobility technique that separates gas-phase ions by their behavior in strong and weak electric fields. FAIMS is easily interfaced with electrospray ionization and has been implemented as an additional separation mode between liquid chromatography (LC) and mass spectrometry (MS) in proteomic studies. FAIMS separation is orthogonal to both LC and MS and is used as a means of on-line fractionation to improve the detection of peptides in complex samples. FAIMS improves dynamic range and concomitantly the detection limits of ions by filtering out chemical noise. FAIMS can also be used to remove interfering ion species and to select peptide charge states optimal for identification by tandem MS. Here, the authors review recent developments in LC-FAIMS-MS and its application to MS-based proteomics.

Targeted Analyte Detection by Standard Addition Improves Detection Limits in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Matrix-assisted laser desorption/ionization (MALDI) has proven an effective tool for fast and accurate determination of many molecules. However, the detector sensitivity and chemical noise compromise the detection of many invaluable low-abundance molecules from biological and clinical samples. To challenge this limitation, we developed a targeted analyte detection (TAD) technique. In TAD, the target analyte is selectively elevated by spiking a known amount of that analyte into the sample, thereby raising its concentration above the noise level, where we take advantage of the improved sensitivity to detect the presence of the endogenous analyte in the sample. We assessed TAD on three peptides in simple and complex background solutions with various exogenous analyte concentrations in two MALDI matrices. TAD successfully improved the limit of detection (LOD) of target analytes when the target peptides were added to the sample in a concentration close to optimum concentration. The optimum exogenous concentration was estimated through a quantitative method to be approximately equal to the original LOD for each target. Also, we showed that TAD could achieve LOD improvements on an average of 3-fold in a simple and 2-fold in a complex sample. TAD provides a straightforward assay to improve the LOD of generic target analytes without the need for costly hardware modifications.

Characterizing odorous emissions using new software for identifying peaks in chemometric models of gas chromatography–mass spectrometry datasets

The task of identifying individual compounds within complex gas chromatography – mass spectrometry (GC–MS) chromatograms is made more difficult by interferences between peaks with similar mass spectra eluting at the same time, typically against a background of chemical and electronic noise. Although chemometric techniques like parallel factor analysis and multivariate curve resolution can help to purify spectra and improve correlations with reference compounds, file incompatibilities between GC–MS acquisition software and modeling software prevent the modeled spectra from being easily compared to spectra in reference libraries. In this paper we present an enhancement to OpenChrom, an open-source software for chromatography and mass spectrometry, which implements the automated cross-matching of modeled spectra to NIST08 and NIST11 mass spectral databases. The benefits of this approach are demonstrated using a complex environmental dataset consisting of non-methane volatile organic compound emissions sampled on an Australian poultry farm.

Neuropeptide analysis with liquid chromatography‐capillary electrophoresis‐mass spectrometric imaging

Herein we report the first attempt of coupling multidimensional separations to matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging detection. Complex neuropeptide mixtures extracted from crustaceans were first fractionated by reversed-phase liquid chromatography (RPLC), and then subjected to a capillary electrophoresis-mass spectrometric imaging platform. With a specific focus on orcokinin family neuropeptides, we demonstrated that these trace-level analytes from complex neural tissue samples can be fully separated from chemical noise and interfering components and visualized as mass spectrometric imaging signals. A total of 19 putative orcokinins were detected, with highly efficient separations within the family being achieved for the first time. The results indicate that two-dimensional separation coupling to mass spectrometric imaging can serve as a novel and powerful tool in proteomics and peptidomics studies.

Surface‐activated chemical ionization–electrospray ionization source improves biomarker discovery with mass spectrometry

Mass spectrometry (MS) is increasingly employed for the discovery of clinical biomarkers. However, due to sensitivity limitations related to in-source ionization yield, many potential biomarkers are not detected by standard mass spectrometers. Therefore, more efficient ion-source technologies are needed to improve MS applications in biomarker discovery. Among novel ion-source technologies, Surface-Activated Chemical Ionization (SACI), although endowed with high sensitivity linked to its ability to reduce chemical noise in mass spectra, has seen limited application in biomarker discovery to date, due to its selectivity for highly polar compounds. However, in combination with an Electrospray Ionization (ESI) source, SACI selectivity can be enlarged in the range of less polar compounds. To validate the new SACI-ESI approach in biomarker discovery, we applied it to a translational setting in oncology. We performed MS profiles of 101 human serum samples from a male population, aged 40 or older, coming to the clinic for prostate cancer evaluation based on multiple PSA exams, digital rectal examination and echography. The SACI-ESI MS spectra were analyzed and classified with an innovative bioinformatic approach based on the MS-search freeware developed in house. Here we demonstrate that the SACI-ESI combination can produce MS spectra with greater sensitivity and lower noise than those obtained with the common ESI alone. We found that the SACI-ESI combination increased the number of detectable compounds and produced better quality of profiles in liquid chromatography (LC) coupled with MS (LC/MS) analysis of human serum samples, improving disease prediction potential. SACI-ESI can facilitate MS-based discovery of potential biomarkers in human serum. Combined with the proposed bioinformatic approach (based on XCMS and NIST data elaboration) for the analysis of the MS spectra obtained, the potential for developing biomarkers with diagnostic capabilities are demonstrated in a prostate cancer diagnosis clinical setting.

Improved mass defect model for theoretical tryptic peptides.

Improvements in the mass accuracy and resolution of mass spectrometers have greatly aided mass spectrometry-based proteomics in profiling complex biological mixtures. With the use of innovative bioinformatics approaches, high mass accuracy and resolution information can be used for filtering chemical noise in mass spectral data. Using our recent algorithmic developments, we have generated the mass distributions of all theoretical tryptic peptides composed of 20 natural amino acids and with masses limited to 3.5 kDa. Peptide masses are distributed discretely, with well-defined peak clusters separated by empty or sparsely populated trough regions. Accurate models for peak centers and widths can be used to filter peptide signals from chemical noise. We modeled mass defects, the difference between monoisotopic and nominal masses, and peak centers and widths in the peptide mass distributions. We found that peak widths encompassing 95% of all peptide sequences are substantially smaller than previously thought. The result has implications for filtering out larger stretches of the mass axis. Mass defects of peptides exhibit an oscillatory behavior which is damped at high mass values. The periodicity of the oscillations is about 14 Da which is the most common difference between the masses of the 20 natural amino acids. To determine the effects of amino acid modifications on our findings, we examined the mass distributions of peptides composed of the 20 natural amino acids, oxidized Met, and phosphorylated Ser, Thr, and Tyr. We found that extension of the amino acid set by modifications increases the 95% peak width. Mass defects decrease, reflecting the fact that the average mass defect of natural amino acids is larger than that of oxidized Met. We propose that a new model for mass defects and peak widths of peptides may improve peptide identifications by filtering chemical noise in mass spectral data.

Improved conductivity image of human lower extremity using MREIT with chemical shift artifact correction

Purpose In performing human MREIT imaging experiments, we addressed two technical issues of the chemical shift artifact and measurement noise. In this study, we present improved conductivity images of in vivo human lower extremity using the chemical shift artifact correction and multi-echo methods.