Automated multiple-layer spotting for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of synthetic polymers utilizing ink-jet printing technology

Recently, a new multiple-layer matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) sample spotting technique for poly(ethylene glycol), offering improved analysis possibilities, was described. In this contribution the application of ink-jet printing to automated, multiple-layer MALDI-TOFMS sample preparation of synthetic polymers is presented, allowing accurate deposition of matrix, additive and analyte solutions. The new sample preparation technique was evaluated for poly(ethylene glycol) as well as poly(methyl methacrylate) standards, and optimized settings for both synthetic polymers have been obtained.     

Automated MALDI-TOF-MS sample preparation in combinatorial polymer research

A new automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) sample spotting technique that allows the integration of MALDI sample preparation in the workflow of combinatorial polymer research is described. The technique is performed utilizing a commercially available synthetic robot and was first evaluated with polymer standards of known composition and later on used for the monitoring of the living cationic ring-opening polymerization of 2-ethyl-2-oxazoline. The spotting was carried out as a multiple layer approach, which offers the ability of complex sample preparation without the requirement of premixing the different components. The described technique reduces the time required for sample preparation and offers the possibility of automated sample spotting during polymerization reactions performed in a synthetic robot. This allows the integration of molecular weight screening and polymer end/group determination utilizing MALDI-TOF-MS as a high-throughput tool in combinatorial polymer research.     

Molecular weight determination of high molecular mass (glyco)proteins using CGE-on-a-chip, planar SDS-PAGE and MALDI-TOF-MS

The molecular weights (MW) of seven (glyco)proteins, of which five were plasma-derived, with MWs higher than 200 kDa were determined with three techniques: CGE-on-a-chip, SDS-PAGE and MALDI-TOF-MS. While the analysis of medium to high MW proteins with SDS-PAGE was an already well-established technique, the usefulness of MALDI-TOF-MS for the exact MW determination of high mass proteins was only partly described in literature so far. CGE-on-a-chip is the newest of all three applied techniques and was so far not applicable. Therefore, it was not evaluated for high MW (glyco)proteins. All proteins were analyzed under nonreducing as well as reducing conditions. In this work, it was demonstrated that all three described techniques were capable of determining the MW of all high molecular weight (glyco)proteins. The noncommercial CGE-on-a-chip assay allowed for the first time the electrophoretic separation of proteins in the MW range from 14 to 1000 kDa. MW assignment was limited to 500 kDa in the case of SDS-PAGE and 660 kDa in the case of the high MW CGE-on-a-chip assay. With the proper matrix and sample preparation, analysis with a standard MALDI-TOF-MS provided accurate MWs for all high MW proteins up to 1?MDa.     

Ultrafiltration for proteomic sample preparation

Proteome analysis represents significant challenges to the existing sample preparation techniques. Traditional methods, such as two-dimensional electrophoresis, typically separate high-molecular-weight proteins while discarding low-molecular-weight species. This approach is well justified considering the complexity of any proteome. However, it is desirable to extract the maximum amount of information from each sample to investigate the entire range of biomolecules. We have demonstrated that ultrafiltration not only improves two-dimensional electrophoresis (2-DE) resolution of the protein fraction but also yields the low-molecular-weight fraction amenable for further analysis by high-resolution mass spectrometry. This approach was successfully adapted to the variety of biological samples including cell and tissue lysates and serum. Therefore, ultrafiltration offers an alternative sample preparation technique that enables more thorough analysis of a proteome.     

A systematic evaluation of chip-based nanoelectrospray parameters for rapid identification of proteins from a complex mixture

HPLC-MS/MS is widely used for protein identification from gel spots and shotgun fractions. Although HPLC has well recognized benefits, this type of sample infusion also has some undesirable attributes: relatively low sample throughput, potential sample-to-sample carryover, time-varying sample composition, and no option for longer sample infusion for longer MS analyses. An automated chip-based ESI device (CB-ESI) has the potential to overcome these limitations. This report describes a systematic evaluation of the information-dependant acquisition (IDA) and sample preparation protocols for rapid protein identification from a complex mixture using a CB-ESI source compared with HPLC-ESI (gradient and isocratic elutions). Cytochrome c and a six-protein mixture (11-117 kDa) were used to develop an IDA protocol for rapid protein identification and to evaluate the effects of sample preparation protocols. MS (1-10 s) and MS/MS (1-60 s) scan times, sample concentration (50-500 fmol/microL), and ZipTipC(18) cleanup were evaluated. Based on MOWSE scores, protein coverage, experimental run time, number of identified proteins, and reproducibility, a 12.5 min experiment (22 cycles, each with one 3 s MS and eight 10 s MS/MS scans) was determined to be the optimal IDA protocol for CB-ESI. This work flow yielded up to 220% greater peptide coverage compared with gradient HPLC-ESI and provided protein identifications with up to a 2-fold higher throughput rate than either HPLC-ESI approach, whilst employing half the amount of sample over the same time frame. The results from this study support the use of CB-ESI as a rapid alternative to the identification of protein mixtures.     

Extraction and derivatization of polar herbicides for GC-MS analyses

A sample preparation procedure including a simultaneous microwave-assisted (MA) extraction and derivatization for the determination of chlorophenoxy acids in soil samples is presented. For a selective and sensitive measurement, an analytical technique such as GC coupled with MS needs to be adopted. For GC analyses, chlorophenoxy acids have to be converted into more volatile and thermally stable derivatives. Derivatization by means of microwave radiation offers new alternatives in terms of shorter derivatization time and reduces susceptibility for the formation of artefacts. Extraction and derivatization into methyl esters (ME) were performed with sulphuric acid and methanol. Due to the novelty of the simultaneous extraction and derivatization assisted by means of microwave radiation, a careful investigation and optimization of influential reaction parameters was necessary. It could be shown that the combination of sulphuric acid and methanol provides a fast sample preparation including an efficient clean up procedure. The data obtained by the described method are in good agreement with those published for the reference material. Finally, compared to conventional heating and also to the standard procedure of the EPA, the sample preparation time could be considerably shortened.     

Detection limits of matrix-assisted laser desorption/ionisation mass spectrometry coupled to chromatography--a new application of solvent-free sample preparation

The detection limits of matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) by semi-online coupling with chromatography were investigated using various mixtures of polyethylene oxides (PEOs) with different end groups. In contrast to the common 'dried-droplet' sample preparation technique, which results in an inhomogeneous sample-to-matrix ratio within the MALDI spot, the used coupling technique offers a very high reproducibility combined with surpassing sensitivity of a few femtograms over a broad range of sample-to-matrix ratios. These results are in correlation with the results of the recently established solvent-free MALDI-TOFMS method utilising the grinding approach and are also of assistance towards the more theoretical aspect of MALDI that suggests that there is no necessity for an analyte incorporation into a matrix crystal for excellent matrix-assistance.     

Multisample preparation methods for the solvent-free MALDI-MS analysis of synthetic polymers

A limitation of any current approach using solvent-free MALDI mass spectrometry is that only one sample at a time can be prepared and transferred to the MALDI-plate. For this reason, multiple-sample preparation approaches for solvent-free MALDI MS analysis of synthetic polymers were developed that are simple and practical. One approach multiplexed sample preparation by simultaneously preparing multiple samples. With this approach, as many as 384 samples could be prepared by addition of analyte, matrix, salt, and 1-mm metal beads to each well of a 384-well disposable bacti plate, capping the plate with the lid and homogenizing all samples simultaneously using a common laboratory vortex device. Besides the time savings achieved by a single vortex step for multiple samples, an additional advantage of this method relative to previously reported solvent-free preparation methods is that the mixing volume per sample is reduced, which allows a reduction in the amount of analyte required. This method, however, still requires the transfer of each homogenized sample to the MALDI plate for subsequent analysis. Here we report a novel approach that combines multiple simultaneous solvent-free sample preparation with automatic sample transfer to the MALDI target plate. This approach reduces the possibility of cross-contamination, the amount of sample and matrix consumed for an analysis, and the time required for preparation of multiple samples. These methods were shown to provide high-quality mass spectra for various synthetic polymer standards with M(n) values to 10 kDa. The methods are efficient in that small sample amounts are required, the sample/salt/matrix ratio is not critical, and the time necessary to achieve sufficient homogenization of multiple samples is less than 5 min.     

Matrix effect in bio-analysis of illicit drugs with LC-MS/MS: Influence of ionization type, sample preparation, and biofluid

The purpose of the present work was to evaluate the synergistic effect of ionization type, sample preparation technique, and bio-fluid on the presence of matrix effect in quantitative liquid chromatography (LC)-MS/MS analysis of illicit drugs by post-column infusion experiments with morphine (10-microg/mL solution). Three bio-fluids (urine, oral fluid, and plasma) were pretreated with four sample preparation procedures [direct injection, dilution, protein precipitation, solid-phase extraction (SPE)] and analyzed by both LC-electrospray ionization (ESI)-MS/MS and LC-atmospheric pressure chemical ionization (APCI)-MS/MS. Our results indicated that both ionization types showed matrix effect, but ESI was more susceptible than APCI. Sample preparation could reduce (clean up) or magnify (pre-concentrate) matrix effect. Residual matrix components were specific to each bio-fluid and interfered at different time points in the chromatogram. We evaluated matrix effect in an early stage of method development and combined optimal ionization type and sample preparation technique for each bio-fluid. Simple dilution of urine was sufficient to allow for the analysis of the analytes of interest by LC-APCI-MS/MS. Acetonitrile protein precipitation provided both sample clean up and concentration for oral fluid analysis, while SPE was necessary for extensive clean up of plasma prior to LC-APCI-MS/MS.     

Overcoming Selectivity and Sensitivity Issues of Direct Inject Electrospray Mass Spectrometry via DAPNe-NSI-MS

Direct inject electrospray mass spectrometry offers minimal sample preparation and a “shotgun” approach to analyzing samples. However, complex matrix effects often make direct inject an undesirable sample introduction technique, particularly for trace level analytes. Highlighted here is our solution to the pitfalls of direct inject mass spectrometry and other ambient ionization methods with a focus on trace explosives. Direct analyte-probed nanoextraction coupled to nanospray ionization mass spectrometry solves selectivity issues and reduces matrix effects while maintaining minimal sample preparation requirements. With appropriate solvent conditions, most explosive residues can be analyzed with this technique regardless of the nature of the substance (i.e., nitroaromatic, oxidizing salt, or peroxide).

Evaluation of automated sample preparation, retention time locked gas chromatography-mass spectrometry and data analysis methods for the metabolomic study of Arabidopsis species

In this paper, automated sample preparation, retention time locked gas chromatography-mass spectrometry (GC-MS) and data analysis methods for the metabolomics study were evaluated. A miniaturized and automated derivatisation method using sequential oximation and silylation was applied to a polar extract of 4 types (2 types×2 ages) of Arabidopsis thaliana, a popular model organism often used in plant sciences and genetics. Automation of the derivatisation process offers excellent repeatability, and the time between sample preparation and analysis was short and constant, reducing artifact formation. Retention time locked (RTL) gas chromatography-mass spectrometry was used, resulting in reproducible retention times and GC-MS profiles. Two approaches were used for data analysis. XCMS followed by principal component analysis (approach 1) and AMDIS deconvolution combined with a commercially available program (Mass Profiler Professional) followed by principal component analysis (approach 2) were compared. Several features that were up- or down-regulated in the different types were detected.     

Ionic liquids as matrices in microfluidic sample deposition for high-mass matrix- assisted laser desorption/ionization mass spectrometry

Sample preparation for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) via a microfluidic deposition device using ionic liquid matrices addresses several problems of standard protocols with crystalline matrices, such as the heterogeneity of sample spots due to the co-crystallization of sample and matrix and the limited capability for high-throughput analysis. Since ionic liquid matrices do not solidify during the measurement, the resulting sample spots are homogeneous. The use of these matrices is also beneficial for automated sample preparation, since crystallization of the matrix is avoided and, thus, no clogging of the spotting device can occur. The applicability of ionic liquids to the analysis of biomolecules with high molecular weights, up to ≈ 1 MDa is shown, as well as a good sensitivity (5 fmol) for recombinant human fibronectin, a protein with a molecular weight of 226 kDa. Microfluidic sample deposition of proteins with high molecular weights will, in the future, allow parallel sample preparation for MALDI-MS and for electron microscopy.     

Identification of volatile basic components in tobacco by headspace liquid-phase microextraction coupled to matrix-assisted laser desorption/ionization with Fourier transform mass spectrometry

A method incorporating headspace liquid-phase microextraction (HS-LPME) coupled to matrix-assisted laser desorption/ionization (MALDI) with Fourier transform mass spectrometry (FTMS) was established to analyze volatile basic components in tobacco. The sample preparation volume for MALDI-MS was compatible with the volume of the solvent microdrop in the HS-LPME procedure. The pH and the polarity of the solvent for HS-LPME were adjusted by choice of the MALDI matrix and matrix additive. Based on the elemental composition and tandem mass spectrometry information, 25 volatile nitrogenous compounds in tobacco were detected and identified. The approach is fast and sensitive, and has the potential for automation for high-throughput analysis. This approach offers an alternative method for analysis of trace volatile organic compounds in complex samples.     

Measurement uncertainty from physical sample preparation: estimation including systematic error

A methodology is proposed, which employs duplicated primary sampling and subsequent duplicated physical preparation coupled with duplicated chemical analyses. Sample preparation duplicates should be prepared under conditions that represent normal variability in routine laboratory practice. The proposed methodology requires duplicated chemical analysis on a minimum of two of the sample preparation duplicates. Data produced from the hierarchical design is treated with robust analysis of variance (ANOVA) to generate uncertainty estimates, as standard uncertainties ('u' expressed as standard deviation), for primary sampling (ssamp), physical sample preparation (sprep) and chemical analysis (sanal). The ANOVA results allow the contribution of the sample preparation process to the overall uncertainty to be assessed. This methodology has been applied for the first time to a case study of pesticide residues in retail strawberry samples. Duplicated sample preparation was performed under ambient conditions on two consecutive days. Multi-residue analysis (quantification by GC-MS) was undertaken for a range of incurred pesticide residues including those suspected of being susceptible to loss during sample preparation procedures. Sampling and analytical uncertainties dominated at low analyte concentrations. The sample preparation process contributed up to 20% to the total variability and had a relative uncertainty (Uprep%) of up to 66% (for bupirimate at 95% confidence). Estimates of systematic errors during physical sample preparation were also made using spike recovery experiments. Four options for the estimation of measurement uncertainty are discussed, which both include and exclude systematic error arising from sample preparation and chemical analysis. A holistic approach to the combination and subsequent expression of uncertainty is advised.     

Fabric Phase Sorptive Extraction: A Paradigm Shift Approach in Analytical and Bioanalytical Sample Preparation

Fabric phase sorptive extraction (FPSE) is an evolutionary sample preparation approach which was introduced in 2014, meeting all green analytical chemistry (GAC) requirements by implementing a natural or synthetic permeable and flexible fabric substrate to host a chemically coated sol–gel organic–inorganic hybrid sorbent in the form of an ultra-thin coating. This construction results in a versatile, fast, and sensitive micro-extraction device. The user-friendly FPSE membrane allows direct extraction of analytes with no sample modification, thus eliminating/minimizing the sample pre-treatment steps, which are not only time consuming, but are also considered the primary source of major analyte loss. Sol–gel sorbent-coated FPSE membranes possess high chemical, solvent, and thermal stability due to the strong covalent bonding between the fabric substrate and the sol–gel sorbent coating. Subsequent to the extraction on FPSE membrane, a wide range of organic solvents can be used in a small volume to exhaustively back-extract the analytes after FPSE process, leading to a high preconcentration factor. In most cases, no solvent evaporation and sample reconstitution are necessary. In addition to the extensive simplification of the sample preparation workflow, FPSE has also innovatively combined the extraction principle of two major, yet competing sample preparation techniques: solid phase extraction (SPE) with its characteristic exhaustive extraction, and solid phase microextraction (SPME) with its characteristic equilibrium driven extraction mechanism. Furthermore, FPSE has offered the most comprehensive cache of sorbent chemistry by successfully combining almost all of the sorbents traditionally used exclusively in either SPE or in SPME. FPSE is the first sample preparation technique to exploit the substrate surface chemistry that complements the overall selectivity and the extraction efficiency of the device. As such, FPSE indeed represents a paradigm shift approach in analytical/bioanalytical sample preparation. Furthermore, an FPSE membrane can be used as an SPME fiber or as an SPE disk for sample preparation, owing to its special geometric advantage. So far, FPSE has overwhelmingly attracted the interest of the separation scientist community, and many analytical scientists have been developing new methodologies by implementing this cutting-edge technique for the extraction and determination of many analytes at their trace and ultra-trace level concentrations in environmental samples as well as in food, pharmaceutical, and biological samples. FPSE offers a total sample preparation solution by providing neutral, cation exchanger, anion exchanger, mixed mode cation exchanger, mixed mode anion exchanger, zwitterionic, and mixed mode zwitterionic sorbents to deal with any analyte regardless of its polarity, ionic state, or the sample matrix where it resides. Herein we present the theoretical background, synthesis, mechanisms of extraction and desorption, the types of sorbents, and the main applications of FPSE so far according to different sample categories, and to briefly show the progress, advantages, and the main principles of the proposed technique.     

Analysis of serine proteases from marine sponges by 2-D zymography

Proteolytic activities isolated from the marine demosponges Geodia cydonium and Suberites domuncula were analyzed by 2-D zymography, a technique that combines IEF and zymography. After purification, a 200 kDa proteolytically active protein band was obtained from G. cydonium when analyzed in gelatin copolymerized 1-D zymograms. The enzymatic activity was quantified using alpha-N-benzoyl-D-arginine p-nitroanilide (BAPNA) as a substrate and corresponded to a serine protease. The protease activity was resistant to urea and SDS. DTT and 2-mercaptoethanol (2-ME) did not significantly change the protease activity, but induced a shift in molecular mass of the proteolytic band to lower M(r) values as detected by zymography. Under mild denaturing conditions, lower M(r) bands (<200 kDa) were identified in 1-D zymograms, suggesting that the protease is composed of subunits which retain the catalytic activity. After 2-D zymography, the protease from G. cydonium revealed a pI of 8.0 and an M(r) shift from 200 to 66 kDa. To contrast these results, a cytosolic sample from S. domuncula was analyzed. The proteolytic activity of this sponge after 2-D zymography corresponded to an M(r) of 40 kDa and a pI of 4.0. The biological function of both sponge proteases is not yet known. This study demonstrates that mild denaturing conditions required for IEF may alter the interpretation of the 2-D zymography, and care must be taken during sample preparation.     

Evaluation of direct analysis in real time mass spectrometry for onsite monitoring of batch slurry reactions

Batch slurry reactions are widely used in the industrial manufacturing of chemicals, pharmaceuticals, petrochemicals and polymers. However, onsite monitoring of batch slurry reactions is still not feasible in production plants due to the challenge in analyzing heterogeneous samples without complicated sample preparation procedures. In this study, direct analysis in real time mass spectrometry (DART-MS) has been evaluated for the onsite monitoring of a model batch slurry reaction. The results suggested that automation of the sampling process of DART-MS is important to achieve quantitative results. With a sampling technique of manual sample deposition on melting point capillaries followed by automatic sample introduction across the helium beam, relative standard deviation (RSD) of the protonated molecule signals from the reaction product of the model batch slurry reaction ranged from 6 to 30%. This RSD range is improved greatly over a sampling technique of manual sample deposition followed by manual sample introduction where the RSDs are up to 110%. Furthermore, with the semi-automated sampling approach, semi-quantitative analysis of slurry samples has been achieved. Better quantification is expected with a fully automated sampling approach.     

Solvent-free MALDI-MS for the analysis of biological samples via a mini-ball mill approach

An efficient, low sample load mini-ball mill (MBM) sample preparation procedure was developed for solvent-free MALDI analysis of peptides and proteins. Picomole sample amounts can be handled conveniently, with 30 s grinding times being sufficient. Matrix purity and molar analyte/matrix ratios are not as critical as with methods employing solvent. Ammonium salt is employed for protonation of the peptide and suppression of sodiation. This strategy allows for peptide mapping and other biochemical manipulations to be performed prior to MBM sample preparation and mass analysis. The analysis of bovine serum albumin (66 kDa) yielded good results, indicating that higher molecular weight proteins are accessible. A semi-solvent-free strategy by the MBM sample preparation method is also described.     

Evaluation of automated direct sample introduction with comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry for the screening analysis of dioxins in fish oil

An automated direct sample introduction technique coupled to comprehensive two-dimensional gas chromatography-time of flight mass spectrometry (DSI-GC x GC/TOF-MS) was applied for the development of a relatively fast and easy analytical screening method for 17 polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) and 4 non-ortho polychlorinated biphenyls (PCBs) in fish oil. Comparison of instrumental performance between DSI-GC x GC/TOF-MS and the traditional gas chromatographic high resolution mass spectrometric (GC-HRMS) method showed good agreement of results for standard solutions analyzed in blind fashion. Relatively high tolerance of the DSI technique for lipids in the final extracts enabled a streamlined sample preparation procedure that only required gel permeation chromatography (GPC) and solid-phase extraction (SPE) cleanup with graphitized carbon black. The sample size for the method was 2g of cod liver oil, which achieved limits of quantitation (LOQs) of 0.019-7.8 pg/g toxic equivalent quotients for the individual PCDD/Fs. Lower detection limits can be achieved by using larger sample size and scaling up the sample preparation procedure, but this adds to the labor, time, solvent consumption, and expense of the approach. However, the streamlined method yielded 0.94 pg/g and 2.3 pg/g LOQs for 2,3,7,8-tetrachloro dibenzofuran (TCDF) and 3,3',4,4',5-pentachloro biphenyl (CB126), which were sufficiently low for regulatory monitoring of 2g samples. Therefore, instead of congener specific analysis, this streamlined analytical screening method for TCDF and CB126 has the potential to monitor fish oil contaminated with dioxin and dioxin-like PCBs at or above current food safety limits. Acceptable recoveries for nearly all analytes at three different spiking levels in fish oil samples were achieved with good repeatability.     

Considerations for quantification of lipids in nerve tissue using matrix-assisted laser desorption/ionization mass spectrometric imaging

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging is a technique that provides the ability to identify and characterize endogenous and exogenous compounds spatially within tissue with relatively little sample preparation. While it is a proven methodology for qualitative analysis, little has been reported for its utility in quantitative measurements. In the current work, inherent challenges in MALDI quantification are addressed. Signal response is monitored over successive analyses of a single tissue section to minimize error due to variability in the laser, matrix application, and sample inhomogeneity. Methods for the application of an internal standard to tissue sections are evaluated and used to quantify endogenous lipids in nerve tissue. A precision of 5% or less standard error was achieved, illustrating that MALDI imaging offers a reliable means of in situ quantification for microgram-sized samples and requires minimal sample preparation.