Chemical Noise Reduction Research Articles

Multiple ion isolation and accumulation events for selective chemical noise reduction and dynamic range enhancement in MALDI imaging mass spectrometry.

Abundant chemical noise in MALDI imaging mass spectrometry experiments can impede the detection of less abundant compounds of interest. This chemical noise commonly originates from the MALDI matrix as well as other endogenous compounds present in high concentrations and/or with high ionization efficiencies. MALDI imaging mass spectrometry of biological tissues measures numerous biomolecular compounds that exist in a wide range of concentrations in vivo. When ion trapping instruments are used, highly abundant ions can dominate the charge capacity and lead to space charge effects that hinder the dynamic range and detection of lowly abundant compounds of interest. Gas-phase fractionation has been previously utilized in mass spectrometry to isolate and enrich target analytes. Herein, we have characterized the use of multiple continuous accumulations of selected ions (Multi CASI) to reduce the abundance of chemical noise and diminish the effects of space charge in MALDI imaging mass spectrometry experiments. Multi CASI utilizes the mass-resolving capability of a quadrupole mass filter to perform multiple sequential ion isolation events prior to a single mass analysis of the combined ion population. Multi CASI was used to improve metabolite and lipid detection in the MALDI imaging mass spectrometry analysis of rat brain tissue.

A review on ion mobility mass spectrometry

Mass Spectrometry can be coupled with ion mobility to get results that cannot be obtained by alone mass spectrometry. This coupled instrument can be used for knowing the separation of isomers, isobars, and conformers, the reduction of chemical noise, and the measurement of ion size. It divides ions into families of ions as well as ions with the same charge and similar structural properties. The four ion mobility separation techniques currently applied to mass spectrometry are described in this article. Low-resolution mobility separation is demonstrated by AIMS. Offering continuous ion monitorings are DMS and FAIMS. TWIMS is a novel IMS technique that has good sensitivity and is well integrated into a commercial mass spectrometer while having modest resolving power. In this review it includes that Many researches has used this technique has it gives results in millisecond and its low cost operation.it has major drawback of contamination of compounds due to atmospheric pressure, complex spectra and interferences aredue to wide spread of ionization.it is not suitable for Non-volatile compound and the repoducubility is1-2%.

Ion Mobility Coupled to a Time-of-Flight Mass Analyzer Combined With Fragment Intensity Predictions Improves Identification of Classical Bioactive Peptides and Small Open Reading Frame-Encoded Peptides.

Bioactive peptides exhibit key roles in a wide variety of complex processes, such as regulation of body weight, learning, aging, and innate immune response. Next to the classical bioactive peptides, emerging from larger precursor proteins by specific proteolytic processing, a new class of peptides originating from small open reading frames (sORFs) have been recognized as important biological regulators. But their intrinsic properties, specific expression pattern and location on presumed non-coding regions have hindered the full characterization of the repertoire of bioactive peptides, despite their predominant role in various pathways. Although the development of peptidomics has offered the opportunity to study these peptides in vivo, it remains challenging to identify the full peptidome as the lack of cleavage enzyme specification and large search space complicates conventional database search approaches. In this study, we introduce a proteogenomics methodology using a new type of mass spectrometry instrument and the implementation of machine learning tools toward improved identification of potential bioactive peptides in the mouse brain. The application of trapped ion mobility spectrometry (tims) coupled to a time-of-flight mass analyzer (TOF) offers improved sensitivity, an enhanced peptide coverage, reduction in chemical noise and the reduced occurrence of chimeric spectra. Subsequent machine learning tools MS2PIP, predicting fragment ion intensities and DeepLC, predicting retention times, improve the database searching based on a large and comprehensive custom database containing both sORFs and alternative ORFs. Finally, the identification of peptides is further enhanced by applying the post-processing semi-supervised learning tool Percolator. Applying this workflow, the first peptidomics workflow combined with spectral intensity and retention time predictions, we identified a total of 167 predicted sORF-encoded peptides, of which 48 originating from presumed non-coding locations, next to 401 peptides from known neuropeptide precursors, linked to 66 annotated bioactive neuropeptides from within 22 different families. Additional PEAKS analysis expanded the pool of SEPs on presumed non-coding locations to 84, while an additional 204 peptides completed the list of peptides from neuropeptide precursors. Altogether, this study provides insights into a new robust pipeline that fuses technological advancements from different fields ensuring an improved coverage of the neuropeptidome in the mouse brain.

Increasing Peak Capacity in Nontargeted Omics Applications by Combining Full Scan Field Asymmetric Waveform Ion Mobility Spectrometry with Liquid Chromatography-Mass Spectrometry.

Full scan field asymmetric waveform ion mobility spectrometry (FAIMS) combined with liquid chromatography and mass spectrometry (LC-FAIMS-MS) is shown to enhance peak capacity for omics applications. A miniaturized FAIMS device capable of rapid compensation field scanning has been incorporated into an ultrahigh performance liquid chromatography (UHPLC) and time-of-flight mass spectrometry analysis, allowing the acquisition of full scan FAIMS and MS nested data sets within the time scale of a UHPLC peak. Proof of principle for the potential of scanning LC-FAIMS-MS in omics applications is demonstrated for the nontargeted profiling of human urine using a HILIC column. The high level of orthogonality between FAIMS and MS provides additional unique compound identifiers with detection of features based on retention time, FAIMS dispersion field and compensation field (DF and CF), and mass-to-charge (m/z). Extracted FAIMS full scan data can be matched to standards to aid the identification of unknown analytes. The peak capacity for features detected in human urine using LC-FAIMS-MS was increased approximately threefold compared to LC-MS alone due to a combination of the reduction of chemical noise and separation of coeluting isobaric species across the entire analytical space. The use of FAIMS-selected in source collision induced dissociation (FISCID) yields fragmentation of ions, which reduces sample complexity associated with overlapping fragmentation patterns and provides structural information on the selected precursor ions.

Doping control analysis of anabolic steroids in equine urine by gas chromatography-tandem mass spectrometry.

Anabolic steroids are banned substances in equine sports. Gas chromatography-mass spectrometry (GC-MS) has been the traditional technique for doping control analysis of anabolic steroids in biological samples. Although liquid chromatography-mass spectrometry (LC/MS) has become an important technique in doping control, the detection of saturated hydroxysteroids by LC-MS remains a problem due to their low ionization efficiency under electrospray. The recent development in fast-scanning gas-chromatography-triple-quadrupole mass spectrometry (GC-MS/MS) has provided a better alternative with a significant reduction in chemical noise by means of selective reaction monitoring. Herein, we present a sensitive and selective method for the screening of over 50 anabolic steroids in equine urine using gas chromatography-tandem mass spectrometry (GC-MS/MS). Copyright © 2016 John Wiley & Sons, Ltd.

Investigations into the Use of a Protein Sensor Assay for Metabolite Analysis.

Rapid and definitive classification of biological samples has application in industrial, agricultural, and clinical settings. Considerable effort has been given to analytical methods to address such applications over the past 50 years, with the majority of successful solutions focusing on a single molecular target. However, in many cases, a single or even a few features are insufficient for accurate characterization or classification. Serum albumin (SA) proteins are a class of cargo-carrying proteins in blood that have evolved to transport a wide variety of metabolites and peptides in mammals. These proteins have up to seven binding sites which communicate allosterically to orchestrate a complex pick-up and delivery system involving a large number of different molecules at any time. The ability of SA proteins to bind multiple molecular species in a sophisticated manner inspired the development of assays to differentiate complex biological solutions. The combination of SA and high-resolution liquid chromatography mass spectrometry (LC-MS) is showing exciting promise as a protein sensor assay (PSA) for classification of complex biological samples. In this study, the PSA has been applied to cells undergoing and recovering from mild oxidative stress. Analysis using traditional LC-MS-based metabolomics failed to differentiate samples into treatment or temporal groups, whereas samples first treated with the PSA were cleanly classified into both correct treatment and temporal groups. The success of the PSA could be attributed to selective binding of metabolites, leading to a reduction in sample complexity and a general reduction in chemical noise. Metabolites important to successful sample classification were often enriched by 100-fold or more yet displayed a wide range of affinities for SA. The end result of PSA treatment is better classification of samples with a reduction in the number of features seen overall. Together, these results demonstrate how the use of a protein-based assay before LC-MS analysis can greatly improve separation and lead to more accurate and successful tracking of the metabolic state in an organism, suggesting potential application in a wide range of fields.

Rapid detection and isotopic measurement of discrete inorganic samples using acoustically actuated droplet ejection and extractive electrospray ionization mass spectrometry

The rapid detection, screening, and isotopic signature analysis of inorganics provide invaluable information for a variety of applications including explosive device detection, nuclear forensics, and environmental monitoring. The coupling of ultrasonic nebulization and extractive electrospray ionization (EESI) enabled the mass spectrometric (MS) detection and analysis of inorganics from microliter sample solution aliquots. Ultrasonic nebulization and acoustic pressure wave focusing within an array of exponential horn structures were utilized for the efficient atomization of discrete liquid samples ranging in volume from 3 μL to 10 μL pipetted aliquots. In conjunction with an electro-flow focusing source for extractive electrospray ionization (EESI), in-source collision-induced dissociation (CID) was utilized to enhance inorganic detection through fragmentation of adducts and reduction in chemical noise from organic compounds. The investigated system enhanced detection of the singly charged elemental cation species and provided accurate measurements of isotopic distributions for a number of metal ions. The extent of CID demonstrated the competition between ligand loss from hydrate clusters and charge reduction from the doubly charged to singly charged cations for the alkaline earth metal ions of strontium and barium. Inorganics were also detected from complex matrices, including synthetic fingerprint material and sediment, without detriment to device operation. The described system provides a versatile tool for the rapid detection, speciation, and isotopic identification of inorganic compounds at nanogram to sub-nanogram levels from microliter aliquots. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA.

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.

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.

Post-optimization of Py-GC/MS data: A case study using a new digital chemical noise reduction filter (NOISERA) to enhance the data quality utilizing OpenChrom mass spectrometric software

Noise is a known drawback in the mass spectrometric analysis of chromatographic data. Different techniques exist to avoid or to remove noise before and after data acquisition. Noise occurs in two different types, electronic and chemical. The former can be lowered by applying smoothing filters. The latter needs more sophisticated methods since the distinction between chemical noise and real chromatographic data is not straightforward. Several approaches have been published with different scopes and algorithms. This work describes a new algorithm (NOISERA – Noise Reduction Algorithm) for a dynamic reduction of chemical noise in mass spectrometric, chromatographic data of nominal mass resolution. It offers an approach to detect and to reduce chemical noise with a minimum of required user interaction and adjustments. Due to the assumption, that chemical noise varies in its intensity and is dependent of the time, the algorithm tries to calculate and reduce noise locally along the retention time axis. Electronic noise will not be covered by the presented algorithm. It can be reduced by applying further filters, since OpenChrom provides methods for smoothing. The presented algorithm NOISERA is capable of reducing noise with minimal user interaction. It combines existing ideas and extends them to achieve a parameter-free chemical noise detection and reduction. NOISERA improves the signal-to-noise ratio of peaks, but as a drawback of all chemical noise filters, it tends to remove either too much, respectively, not enough data from chromatograms than necessary. That is why the algorithm should not be used without supervision of an analyst. The noise reduction filter NOISERA is available as a plug-in for OpenChrom and is released under the Eclipse Public License 1.0 (EPL). OpenChrom is available free of charge at http://www.openchrom.net. The noise reduction algorithm NOISERA is included in the latest OpenChrom release.

Reduction of Chemical Noise in Electrospray Ionization Mass Spectrometry by Supplemental IR Activation

Supplemental infrared (IR) activation was applied to reduce background chemical noise and increase analyte ion signal in a linear ion trap mass spectrometer. Peptides, proteins, and small molecules were all introduced by electrospray ionization, and when regions of chemical noise were isolated and subjected to IR irradiation, protonated analyte molecules were observed in the product ion mass spectra. By isolating the entire mass range (e.g., m/z 400-2000) and then irradiating all ions in the trap, supplemental IR activation increased the signal of singly protonated peptides by almost 70% and by 40%-55% for the lower charge states of cytochrome c. This increase in analyte ion signal was less dramatic for the higher charge states of peptides and proteins. The chemical noise present in the mass spectra is attributed to incomplete desolvation of the electrospray, as the abundance of the protonated peptides observed upon supplemental IR activation of the chemical noise decreased with higher inlet capillary temperatures. Collision activation was not as effective for desolvating the ions present in the chemical noise.

Alternative Reagents for Chemical Noise Reduction in Liquid Chromatography–Mass Spectrometry Using Selective Ion–Molecule Reactions

Reduction of ionic chemical background noise based on selective gas-phase reactions with chosen neutral reagents has been proven to be a very promising approach in liquid chromatography-mass spectrometry (LC-MS). In this study further investigations on alternative reagents including the disulfides (dimethyl disulfide, diethyl disulfide, methyl propyl disulfide), dimethyl trisulfide, ethylene oxide, and butadiene monoxide, for example, have been carried out. Tandem mass spectrometric studies of ion/molecule reactions indicate that-besides dimethyl disulfide-ethylene oxide and butadiene monoxide also exhibit very efficient reactions with background ions. Furthermore, it is confirmed that the reactions are very selective according to the test with some analyte ions. In contrast to its rapid reactions with background ions, ethylene oxide does not react, or reacts much less, with these analytes. Therefore, it can be used as an alternative reagent for noise reduction. Although reactions of the other tested neutral reagents with background ions are evaluated, they are generally not suitable as reagents for this purpose because of lack of reactivity or dramatic ion losses during reactions.

Ion mobility–mass spectrometry

This review article compares and contrasts various types of ion mobility-mass spectrometers available today and describes their advantages for application to a wide range of analytes. Ion mobility spectrometry (IMS), when coupled with mass spectrometry, offers value-added data not possible from mass spectra alone. Separation of isomers, isobars, and conformers; reduction of chemical noise; and measurement of ion size are possible with the addition of ion mobility cells to mass spectrometers. In addition, structurally similar ions and ions of the same charge state can be separated into families of ions which appear along a unique mass-mobility correlation line. This review describes the four methods of ion mobility separation currently used with mass spectrometry. They are (1) drift-time ion mobility spectrometry (DTIMS), (2) aspiration ion mobility spectrometry (AIMS), (3) differential-mobility spectrometry (DMS) which is also called field-asymmetric waveform ion mobility spectrometry (FAIMS) and (4) traveling-wave ion mobility spectrometry (TWIMS). DTIMS provides the highest IMS resolving power and is the only IMS method which can directly measure collision cross-sections. AIMS is a low resolution mobility separation method but can monitor ions in a continuous manner. DMS and FAIMS offer continuous-ion monitoring capability as well as orthogonal ion mobility separation in which high-separation selectivity can be achieved. TWIMS is a novel method of IMS with a low resolving power but has good sensitivity and is well intergrated into a commercial mass spectrometer. One hundred and sixty references on ion mobility-mass spectrometry (IMMS) are provided.

Biological Variation of the Platelet Proteome in the Elderly Population and Its Implication for Biomarker Research

Knowledge about the extent of total variation experienced between samples from different individuals is of great importance for the design of not only proteomics but every clinical study. This variation defines the smallest statistically significant detectable signal difference when comparing two groups of individuals. We isolated platelets from 20 healthy human volunteers aged 56-100 years because this age group is most commonly encountered in the clinics. We determined the technical and total variation experienced in a proteome analysis using two-dimensional DIGE with IPGs in the pI ranges 4-7 and 6-9. Only spots that were reproducibly detectable in at least 90% of all gels (n = 908) were included in the study. All spots had a similar technical variation with a median coefficient of variation (cv) of about 7%. In contrast, spots showed a more diverse total variation between individuals with a surprisingly low median cv of only 18%. Because most known biomarkers show an effect size in a 1-2-fold range of their cv, any future clinical proteomics study with platelets will require an analytical method that is able to detect such small quantitative differences. In addition, we calculated the minimal number of samples (sample size) needed to detect given protein expression differences with statistical significance.

Using ProSight PTM and Related Tools for Targeted Protein Identification and Characterization with High Mass Accuracy Tandem MS Data

ProSight PTM v2.0, neuroProSight, and the Sequence Gazer allow the identification and characterization of proteins from high mass accuracy tandem mass spectrometric data of intact proteins and large peptides. Input data consists of one or more neutral precursor ion masses and a set of neutral b/y or c/z(.) fragment ions masses. This data is compared against "shotgun annotated" proteome databases or known protein sequences. With these tools it is possible to not only identify unknown proteins, but to determine the location of post-translational modifications (PTM) with 100% sequence coverage. Collectively, the tools create a search environment that allows five different search modes, including absolute mass and sequence tag searching, which are conveniently employed via a graphical user interface. Data management and chemical noise reduction tools are also available. These tools provide a complete environment for the identification and characterization of proteins from high resolution tandem mass spectrometry of intact proteins and large peptides.

A one-way hydrophobic surface foil as sample support for MALDI and off- line CZE/MALDI mass spectrometry: An alternative for low and high molecular mass compounds

A one-way multilayered flexible hydrophobic foil, fixed onto a standard microtiter-format MALDI target, has been utilized as a sample support for UV matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric experiments as well as for the automated off- line coupling of capillary zone electrophoresis (CZE) with MALDI. Various matrices as well as preparation techniques on this polar solution-repellent foil were evaluated with regard to matrix suppression effects, sensitivity and crystallization of deposited samples as well as drop migration on the surface. The results were compared with those yielded on the conventional stainless steel targets. It turned out that this foil is a sample support of choice due to significant improvements in chemical noise reduction, spot area reduction, sensitivity and no drop migration dealing with low molecular mass compounds such as tryptic peptide mixtures, small organic synthetic biomolecules (200–700 Da) as well as intact proteins. Furthermore the foil was a useful MALDI sample surface for the deposition of CZE peptide fractions in proteomics applications.

Method To Reduce Chemical Background Interference in Atmospheric Pressure Ionization Liquid Chromatography−Mass Spectrometry Using Exclusive Reactions with the Chemical Reagent Dimethyl Disulfide

The interference of chemical background ions (chemical noise) has been a problem since the inception of mass spectrometry. We present here a novel method to reduce the chemical noise in LC-MS based on exclusive gas-phase reactions with a reactive collision gas in a triple-quadrupole mass spectrometer. Combined with the zero neutral loss (ZNL) scan of a triple-quadrupole mass spectrometer, the reactive chemical noise ions can be removed because of shifts of mass-to-charge ratios from the original background ions. The test on various classes of compounds with different functional groups indicates a generic application of this technique in LC-MS. The preliminary results show that a reduction of the level of LC-MS base-peak chromatographic baseline by a factor up to 40 and an improvement of the signal-to-noise ratio by a factor up to 5-10 are achieved on both commercial and custom-modified triple-quadrupole LC-MS systems. Application is foreseen in both quantitative and qualitative trace analysis. It is expected that this chemical noise reduction technique can be optimized on a dedicated mass spectrometric instrumentation which incorporates both a chemical reaction cell for noise reduction and a collision stage for fragmentation.

Scrubbing Ions with Molecules: Kinetic Studies of Chemical Noise Reduction in Mass Spectrometry Using Ion−Molecule Reactions with Dimethyl Disulfide

The kinetics and product distributions of the reactions of dimethyl disulfide (DMDS) have been investigated with a group of chemical background ions commonly observed in atmospheric pressure ionization (API) mass spectrometry (MS) in order to assess the value of this molecule in filtering (or "scrubbing") these ions by changing their mass/charge (m/z) ratio. The measurements were taken with a novel electrospray ionization/selected ion flow tube/QqQ tandem mass spectrometer. The background ions studied include those with m/z 42 (protonated acetonitrile, ACN), 83 (protonated ACN dimer), 99 (protonated phosphoric acid), 117 (water cluster of m/z 99), 131 (methanol cluster of m/z 99), 149 (protonated phthalic anhydride, formed from the phthalates), and 327 (protonated triphenyl phosphate). In addition, reactions of DMDS have been studied with two model analytes--protonated caffeine and doubly protonated bradykinin--in order to assess the selectivity of DMDS reactivity. All the measurements were taken at 295 +/- 2 K in helium buffer gas at a pressure of 0.35 +/- 0.01 Torr. DMDS was observed to react efficiently with m/z 42 (ACNH+), 149 (from phthalates), and 99 (protonated phosphoric acid), with k/kc=0.91, 0.47, and 0.38, respectively. Only proton transfer was observed with ACNH+, followed by the secondary reaction of [DMDSH]+ with DMDS to yield [CH3S-S(CH3)-SCH3]+. Ligation of DMDS was the dominant primary channel observed for the reaction of the m/z 149 background ion; however, some proton transfer also was observed. Both of these primary product ions react further with DMDS to yield [CH3S-S(CH3)-SCH3]+, the structure of which we have determined computationally using DFT calculations. Only the sequential ligation with two DMDS molecules was observed for the reaction of the m/z 99 ion. Reactions of DMDS with m/z 117 [H3PO4 + H + H2O]+ and m/z 131 [H3PO4 + H + MeOH]+ were observed to proceed with k/kc=0.71 and 0.058, respectively. Ligand substitution of DMDS for H2O predominated ( approximately 94%) over DMDS ligation ( approximately 6%) in the reaction with m/z 117, while only DMDS ligation was observed for the reaction of m/z 131 with DMDS. In contrast, the reactions of DMDS with ions of m/z 83 (protonated dimer of ACN) and 327 (protonated triphenyl phosphate) were extremely inefficient, with k/kc=0.0042 and 0.0079, respectively. The higher reactivity of DMDS toward ACNH+ (m/z 42) compared to (ACN)2H+ (m/z 83) is attributed to the lower proton affinity of the unsolvated ACN. The reactivity of DMDS toward the two model analyte ions studied-protonated caffeine and doubly protonated bradykinin-was negligible, with k/kc=0.0073 and 0.010, for the respective reactions. These results suggest that, under appropriate reagent pressure conditions, DMDS can be an appropriate reagent for chemically filtering out many common API-MS background ions, without significantly affecting the observed intensity of analyte peaks.

Pyridinium-based ionic liquid matrices can improve the identification of proteins by peptide mass-fingerprint analysis with matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry has become an indispensable tool for identification of proteins by peptide mass-fingerprint analysis. Selection of the matrix, addition of matrix additives, and sample-preparation techniques are known to affect the quality of the spectra and hence protein identification. We investigated the effect of pyridine as matrix additive for the commonly used crystalline matrix alpha-cyano-4-hydroxycinnamic acid (CCA), forming a pyridinium based ionic liquid matrix, on the mass spectra of synthetic peptides and tryptic protein digests. Beside the equimolar mixture of CCA and pyridine, the effect of addition of substoichiometric amounts of the base to the acid was tested. Optimum results in terms of signal-to-noise ratios, reduction of chemical noise, and reduced formation of alkali adducts and matrix clusters were observed for the matrix CCA-pyridine in the molar ratio 2:1. The optimized ionic liquid matrix was used for identification of tryptic digests of six model proteins and for identification of a protein extracted from a two-dimensional gel with the proteome of the bacterium Corynebacterium glutamicum, and shown to facilitate protein identification, yielding higher scores and increased sequence coverage compared with pure CCA. Thus CCA-Py 2:1 is a potential alternative for identification and characterization of proteins by peptide mass-fingerprint analysis.

Enhanced extraction capacity and chemical noise reduction in solid‐phase microextraction

Solid-phase microextraction fibres with different lengths, coatings (polydimethylsiloxane, polyacrylate, Carbowax/divinylbenzene), film thicknesses, and mounting techniques were examined in combination with GC-MS with regard to their enhanced extraction capacities and fibre 'bleeding'. A series of phenols and halogenated aromatics with diverse physicochemical properties were investigated to characterize the effects of the enhanced extraction capacities of solid-phase microextraction fibres. Fibre extension was found to be effective for the microextraction of compounds with high log Kow values, whereas increasing both coating thickness and fibre length is most effective for the microextraction of more polar compounds such as phenols. Almost no bisphenol A was released when custom-made polydimethylsiloxane fibres were used, finally eliminating a drawback of endocrine disrupter analysis by solid-phase microextraction.