Prestructured MALDI-MS sample supports

Improving the signal intensity and sensitivity of MALDI mass spectrometry by using nanoliter spots deposited by induction-based fluidics

A new contact-free, small droplet deposition method using an induction-based fluidics (IBF) technique to dispense nanoliter drops is described and evaluated for sample preparation in matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The signal intensities available when using nanoliter spots are greater than those obtained with normal, microliter spots when the same amount of analyte is used. When using an ionic-liquid matrix, the improvement in sensitivity is equal to the concentration enhancement that was achieved by using smaller quantities of matrix. When using a conventional solid matrix, however, the increase in signal intensity shows a more complicated relationship to concentration. The approach of nanoliter deposition also supports multiple spotting to increase sample concentration and, thus, sample signal intensity. Nanoliter spotting not only improves the signal intensity and sensitivity achieved by MALDI-MS but also allows a major fraction of trace samples to be saved for other experiments, thus expanding the application of MALDI-MS to biological studies where sample quantity is limited.

Quantitative analysis of antiretroviral drugs in lysates of peripheral blood mononuclear cells using MALDI-triple quadrupole mass spectrometry

We report here on the use of a prototype matrix-assisted laser desorption/ionization (MALDI)-triple quadrupole mass spectrometer for quantitative analysis of six antiretroviral drugs in lysates of peripheral blood mononuclear cells (PBMC). Of the five investigated MALDI matrixes, 2,5-dihydroxybenzoic acid (DHB) and the novel 7-hydroxy-4-(trifluoromethyl)coumarin (HFMC) showed the broadest application ranges for the antiretroviral drugs. For DHB, the mean relative errors ranged from 8.3 (ritonavir) to 4.3% (saquinavir). The mean precisions (CV) ranged from 17.3 (nevirapine) to 10.8% (saquinavir). The obtained lower limits of quantitation (LLOQ) readily allow clinical applications using just 1 million PBMC from HIV-infected patients under therapy. The new matrix HFMC was used for quantitative analysis of the HIV protease inhibitor indinavir using a stainless steel target plate as well as a target plate with a novel, strongly hydrophobic fluoropolymer coating. Using the coated target plate, the mean relative error improved from 10.1 to 4.6%, the mean precision from 33.9 to 9.9% CV, and the LLOQ from 16 to 1 fmol. In addition, the measurement time for one spot went down from 6 to only 2.5 s.

Antigen receptor editing in anti-DNA transitional B cells deficient for surface IgM

In response to encounter with self-Ag, autoreactive B cells may undergo secondary L chain gene rearrangement (receptor editing) and change the specificity of their Ag receptor. Knowing at what differentiative stage(s) developing B cells undergo receptor editing is important for understanding how self-reactive B cells are regulated. In this study, in mice with Ig transgenes coding for anti-self (DNA) Ab, we report dsDNA breaks indicative of ongoing secondary L chain rearrangement not only in bone marrow cells with a pre-B/B cell phenotype but also in immature/transitional splenic B cells with little or no surface IgM (sIgM(-/low)). L chain-edited transgenic B cells were detectable in spleen but not bone marrow and were still found to produce Ab specific for DNA (and apoptotic cells), albeit with lower affinity for DNA than the unedited transgenic Ab. We conclude that L chain editing in anti-DNA-transgenic B cells is not only ongoing in bone marrow but also in spleen. Indeed, transfer of sIgM(-/low) anti-DNA splenic B cells into SCID mice resulted in the appearance of a L chain editor (Vlambdax) in the serum of engrafted recipients. Finally, we also report evidence for ongoing L chain editing in sIgM(low) transitional splenic B cells of wild-type mice.

Role of the support material on laser desorption/ionization mass spectra

We report the results of experimental studies on the effects of sample supports in laser desorption/ionization mass spectrometry (LDI-MS). LDI time-of-flight (TOF) mass spectra obtained for C(60) and insulin samples deposited onto standard stainless steel substrate and/or onto some non-metallic materials (glass, scotch tape, floppy disc foil, Teflon foil, photocopy film), all recorded under identical, typical experimental conditions, have been compared with regard to their intensity and quality. The LDI investigations show that compared with stainless steel, glass and floppy disc foil sample supports boost (2-3.5 times) ion yields for C(60)(+) and C(60)(-) ions, respectively. The stainless steel and scotch tape sample supports are the best for the mass resolution of positive ions and the formation of (C(60))(n)(-) (n <or= 4) cluster ions, respectively. In the case of detection of insulin by matrix-assisted laser desorption/ionization (MALDI) we did not observe significant differences in sensitivity for the support materials tested. A mechanism of ion formation in the desorption plume is suggested.

MALDI MS sample preparation by using paraffin wax film: systematic study and application for peptide analysis

Recently developed sample preparation techniques employing hydrophobic sample support have improved the detection sensitivity and mass spectral quality of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). These methods concentrate the samples on target by minimizing the sample area via the solvent repellent effect of the target surface. In the current study, we employed the use of paraffin wax film (Parafilm M) for improved MALDI MS analysis of low-abundance peptide mixtures, including neuronal tissue releasate and protein tryptic digests. This thin film was found to strongly repel polar solvents including water, methanol, and acetonitrile, which enabled the application of a wide range of sample preparation protocols that involved the use of various organic solvents. A "nanoliter-volume deposition" technique employing a capillary column has been used to produce tiny ( approximately 400 microm) matrix spots of 2,5-dihydroxybenzoic acid on the film. By systematically optimizing the sample volume, solvent composition, and film treatment, the Parafilm M substrate in combination with the nanoliter-volume matrix deposition method allowed dilute sample to be concentrated on the film for MALDI MS analysis. Peptide mixtures with nanomolar concentrations have been detected by MALDI time-of-flight and MALDI Fourier transform ion cyclotron resonance mass spectrometers. Overall, the use of Parafilm M enabled improved sensitivity and spectral quality for the analysis of complex peptide mixtures.

On-target sample preparation of 4-sulfophenyl isothiocyanate-derivatized peptides using AnchorChip Targets

De novo sequencing of tryptic peptides by post source decay (PSD) or collision induced dissociation (CID) analysis using MALDI TOF-TOF instruments is due to the easy interpretation facilitated by the introduction of N-terminal sulfonated derivatives. Recently, a stable and cheap reagent, 4-sulfophenyl isothiocyanate (SPITC), has been successfully used for N-terminal derivatization. Previously described methods have always used desalting and concentration by reverse-phase chromatography prior to mass spectrometric analysis. Here we present an on-target sample preparation method based on AnchorChip target technology. The method was optimized for reduction of by-products and sensitivity with SPITC-derivatized tryptic BSA peptides, and successfully applied to protein identification from silver-stained two-dimensional electrophoretic gels of fish liver extracts. The method is simple and sensitive and allowed protein identification based on de novo sequencing and BLAST search from species with limited sequence information.

Protein arrays on patterned porous gold substrates interrogated with mass spectrometry: detection of peptides in plasma

Methyl- and carboxy-terminated self-assembled monolayers (SAMs) were custom-patterned on porous gold substrates with equipment commonly used to print protein arrays, without complex surface chemistry protocols. Proteins were covalently immobilized on hydrophilic carboxy-terminated SAM spots, while the remainder of the surface was superhydrophobic due to the roughened gold surface and the methyl-terminated SAM. The resistance of these patterns to biofouling and the effective containment of MALDI matrix solution within the hydrophilic spot made these surfaces amenable to analyzing protein-peptide binding with mass spectrometry. A model system of the affinity peptides HA, cmyc, and V5 and their corresponding antibodies was used to demonstrate the utility of the patterned porous gold. Mass spectrometry (MS) and tandem mass spectrometry (MS/MS) matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectra and images obtained reflected the effective capture of the affinity peptides directly from spiked bovine plasma.

A novel approach using MALDI-TOF/TOF mass spectrometry and prestructured sample supports (AnchorChip Technology) for proteomic profiling and protein identification

Mass spectrometry (MS)-based proteomic profiling and protein identification has become a powerful tool for the discovery of new disease biomarkers. Among the MS platforms, matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) MS offers high sample throughput and the flexibility to couple with different off-line sample fractionation techniques. Here, we present a strategy using MALDI-TOF/TOF MS to analyze fractionated human serum samples for proteomic profiling and then identify serum peptides from these proteomic profiles. We achieve the profiling analyses by using different functionalized magnetic beads to enrich specific subsets of serum proteins/peptides based on their absorption to these beads. This step is followed by elution, transfer onto prestructured sample supports (AnchorChip targets), and analysis in a MALDI-TOF/TOF mass spectrometer. Selected serum peptides are then analyzed in the tandem MS (TOF/TOF) mode to generate fragment ions for determination of their amino acid sequences. We have demonstrated that using this approach, proteomic profiling and protein identification can be done in a single MS instrument.

Rapid and automatic on-plate desalting protocol for MALDI-MS: using imprinted hydrophobic polymer template

A novel protocol of rapid and automatic on-plate desalting (OPD) and peptide concentration for 2-DE-MALDI-MS has been developed by the approach of templating the hydrophobic polymer solution over Kapton-etched mask. For the template technique, small hydrophobic polymer [linear poly(methyl methacrylate) (PMMA), PMMA derivatized with fullerene-C60 (PMMA-C60), linear polystyrene (PSt), or PSt derivatized with fullerene-C60 (PSt-C60)] spots (990 microm od) are patterned at the centers of stainless MALDI plate wells (1400 microm id). Tryptic-peptide solution with no predesalting was dropped onto the central hydrophobic spots, resulting in a concentration of proteolytic peptides on the hydrophobic polymer surface with a reduced spot size. The dried peptide layer was then covered subsequently with over-volume matrix solution, causing the removal of redissolved salts from the spot center to the spot edge by means of a natural "outward flow." The proposed OPD protocol exhibited a dramatic enhancement in S/N up to 850 for 14 fmol BSA digests in the coexistence of 100 mM salts, compared with barely detectable peaks in ordinary way. This analysis has shown that the success rate of identification was increased by two-fold for low abundance proteins in the human liver tissue with no need for the conventional ZipPlate desalting strategy.

Application of fluorescence difference gel electrophoresis technology in searching for protein biomarkers in chick myopia

The lens-induced myopia (LIM) in response to concave lens (negative lens) is a well established animal model for studying myopia development. However, the exact visual and neurochemical signaling mechanisms involving myopic eye growth are yet to be elucidated. The feasibility of applying a novel two-dimensional fluorescence difference gel electrophoresis technique for global protein profilings and a search for differential protein expressions in LIM were explored in the present study. Two-dimensional polyacrylamide gel electrophoresis was performed employing a "minimal Lysine labeling" approach and a reverse CyeDye experimental protocol using retinal tissue from chicks. The retinal protein profiles between myopic and control eyes were found to be very similar. More than a thousand protein spots could be detected on a 2D gel. Sixteen and ten protein spots were found to be up-regulated and down-regulated respectively in the myopic eyes according to our preset criteria with the inclusion of an internal pool standard. About 65% of those filtered spots could be successfully identified by peptide mass fingerprinting by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry . Most of the differentially expressed proteins were found to be related to cytoskeletal or oxidative functions. According to the prediction of subcellular locations, most of them (about 84%) were classified as cytoplasmic proteins. The cellular functions for those differentially expressed proteins were reported and their possible involvements in the compensated eye growth were discussed. We have optimized a workable protocol for the study of the differential retinal protein expressions in the LIM using 2D-DIGE approach which was shown to have a number of advantages over the traditional 2D electrophoresis technique.

An improved method of sample preparation on AnchorChip targets for MALDI-MS and MS/MS and its application in the liver proteome project

An improved method for sample preparation for MALDI-MS and MS/MS using AnchorChip targets is presented. The method, termed the SMW method (sample, matrix wash), results in better sensitivity for peptide mass fingerprinting as well as for sequencing by MS/MS than previously published methods. The method allows up-concentration and desalting directly on the mass spectrometric target and should be amenable for automation. A draw back caused by extensive oxidation of methionine and tryptophan in the SMW method can be alleviated by the addition of n-octyl glucopyranoside and DTT to the sample solution. The method was validated for protein identification from a 2-DE based liver proteome study. The SMW method resulted in identification of many more proteins and in most cases with a better score than the previously published methods.

High MS-compatibility of silver nitrate-stained protein spots from 2-DE gels using ZipPlates and AnchorChips for successful protein identification

The availability of easy-to-handle, sensitive, and cost-effective protein staining protocols for 2-DE, in conjunction with a high compatibility for subsequent MS analysis, is still a prerequisite for successful proteome research. In this article we describe a quick and easy-to-use methodological protocol based on sensitive, homogeneous, and MS-compatible silver nitrate protein staining, in combination with an in-gel digestion, employing the Millipore 96-well ZipPlate system for peptide preparation. The improved quality and MS compatibility of the generated protein digests, as compared to the otherwise weakly MS-compatible silver nitrate staining, were evaluated on real tissue samples by analyzing 192 Coomassie-stained protein spots against their counterparts from a silver-stained 2-DE gel. Furthermore, the applicability of the experimental setup was evaluated and demonstrated by the analysis of a large-scale MALDI-TOF MS experiment, in which we analyzed an additional ~1000 protein spots from 2-DE gels from mouse liver and mouse brain tissue.

Wash-free in-situ self-desalting and peptide enrichment by block copolymer analyzed with MALDI-TOFMS

A novel technique of simultaneous peptide enrichment and wash-free in-situ self-desalting for MALDI analysis is reported, where a newly synthesized block copolymer with a microphase-separated configuration is applied to embed salts with its hydrophilic domain of poly(ethylene oxide) and concentrate peptides with its hydrophobic domain of polysulfone.

Sample preparation by in-gel digestion for mass spectrometry-based proteomics

The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by "in-gel digestion" has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches.

Reproducibility in Protein Profiling by MALDI-TOF Mass Spectrometry

Background: Protein profiling with high-throughput sample preparation and MALDI-TOF MS analysis is a new potential tool for diagnosis of human diseases. However, analytical reproducibility is a significant challenge in MALDI protein profiling. This minireview summarizes studies of reproducibility of MALDI protein profiling and current approaches to improve its analytical performance.

Methods: The PubMed database was searched using combinations of the following search terms: MALDI, SELDI, reproducibility, variation, precision, peak intensity, quantification, peptide, biomarkers, and proteomics. Acceptance criteria were detailed reports on the reproducibility with MALDI protein profiling and studies describing efforts to improve the analytical performance with this technology.

Results: The reported intraexperiment CVs of the peak intensity vary highly between individual protein peaks, with the reported mean CV of the peak intensity varying among studies from 4% to 26%. There is additional interexperiment variation in peak intensity. Current approaches to improve the analytical performance of MALDI protein profiling include automated sample processing, extensive prefractionation strategies, immunocapture, prestructured target surfaces, standardized matrix (co)crystallization, improved MALDI-TOF MS instrument components, internal standard peptides, quality-control samples, replicate measurements, and algorithms for normalization and peak detection.

Conclusions: Further evaluation and optimization of MALDI-TOF MS is recommended before use in routine analysis.

Liquid matrix deposition on conductive hydrophobic surfaces for tuning and quantitation in UV-MALDI mass spectrometry

With its highly fluctuating ion production matrix-assisted laser desorption/ionization (MALDI) poses many practical challenges for its application in mass spectrometry. Instrument tuning and quantitative ion abundance measurements using ion signal alone depend on a stable ion beam. Liquid MALDI matrices have been shown to be a promising alternative to the commonly used solid matrices. Their application in areas where a stable ion current is essential has been discussed but only limited data have been provided to demonstrate their practical use and advantages in the formation of stable MALDI ion beams. In this article we present experimental data showing high MALDI ion beam stability over more than two orders of magnitude at high analytical sensitivity (low femtomole amount prepared) for quantitative peptide abundance measurements and instrument tuning in a MALDI Q-TOF mass spectrometer. Samples were deposited on an inexpensive conductive hydrophobic surface and shrunk to droplets <10 nL in size. By using a sample droplet <10 nL it was possible to acquire data from a single irradiated spot for roughly 10,000 shots with little variation in ion signal intensity at a laser repetition rate of 5-20 Hz.

High-speed, high-resolution monolithic capillary LC-MALDI MS using an off-line continuous deposition interface for proteomic analysis

High-speed, high-resolution LC separations, using a poly(styrene-divinylbenzene) monolithic column, have been coupled to MALDI MS and MS/MS through an off-line continuous deposition interface. The LC eluent was mixed with alpha-cyano-4-hydroxycinnamic acid matrix solution and deposited on a MALDI plate that had been precoated with nitrocellulose. Deposition at subatmospheric pressure (80 Torr) formed a 250-microm-wide serpentine trace with uniform width and microcrystalline morphology. The deposited trace was then analyzed in the MS mode using a MALDI-TOF/TOF MS instrument. Continuous deposition allowed interrogation of the separation with a high data sampling rate in the chromatographic dimensions, thus preserving the high resolution of narrow peaks (3-5-s peak width at half-height) of the fast monolithic LC. No extracolumn band broadening due to the deposition process was observed. Over 2000 components were resolved in a 10-min linear gradient separation of the model sample, and 386 unique peptides were identified in the subsequent MS/MS analysis. The continuous deposition interface allows the coupling of high-resolution separations to MALDI MS without degradation in separation efficiency, thus enabling high-throughput proteome analysis.

A computer algorithm for the identification of protein interactions from the spectra of masses (PRISM)

A new algorithm is reported to assist with the identification of protein interaction domains by comparing pairs of MALDI mass spectra recorded for protein digests treated with a binding partner versus an untreated control. Known as PRISM, for protein interactions from the spectra of masses, the algorithm imports m/z versus peak area data directly from a pair of MALDI mass spectra recorded for the control and reaction sample. The algorithm is shown to be able to successfully identify antigenic determinants for protein antigens within mixed protein digests. The algorithm has general utility for the comparative analysis of differences within any two mass spectra of any type and is easily implemented using a simple, intuitive graphical user interface (GUI).

Proteome analysis after co-administration of clozapine or haloperidol to MK-801-treated rats

MK-801, a glutamergic, N-methyl-D-aspartate (NMDA)-receptor antagonist that mediates neurotransmission and has psychotomimetic properties, giving schizophrenia-like symptom. The objective of this study was to investigate the effects on the thalamic and cortical proteome of one typical (haloperidol) and one atypical (clozapine) antipsychotic drug in interaction with MK-801 in rats. Rats received subcutaneous injections of MK-801 or vehicle (controls) or MK-801 together with concurrent administration of haloperdol or clozapine for eight days. Protein samples from thalamus and cortex were analyzed with two-dimensional gel electrophoresis in combination with mass spectrometry. MK-801 induced alterations in the levels of three proteins in both cortex and thalamus. Clozapine reversed all the protein changes. Haloperidol reversed two. Both antipsychotics induced new protein changes in both cortex and thalamus not seen after MK-801-treatment by alone. In conclusion, the MK-801 animal model shows potential for investigation of different antipsychotic drugs and biochemical treatment effects in schizophrenia.

Evaluation of an on-target sample preparation system for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in conjunction with normal-flow peptide high-performance liquid chromatography for peptide mass fingerprint analyses

Large-scale mass spectrometry (MS)-based proteomic analyses require high-throughput sample preparation techniques due to the increasing numbers of samples that make up a typical proteomics experiment. Moreover, extensive sample pre-treatment steps are necessary prior to MS acquisition for even the most rapid and robust MS-based proteomics methodology, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS followed by peptide mass fingerprinting (PMF) analysis. These include sample purification and fractionation, removal of digestion buffers or solvents, and spotting of sample with matrix onto the MALDI target. These multiple steps of time-consuming sample handling can result in high overall analysis costs and the likelihood of sample contamination and loss. In order to overcome some of these limitations in sample processing, we have investigated the use of a novel, simple, inexpensive 96-well elastomeric array that affixes to a MALDI target to create an on-target 96-well plate that accommodates a high solution volume (ca. 200 microL), thereby enabling the on-target processing of samples for MALDI-TOFMS. We explored several factors that influence MALDI sample preparation: type of matrix, solution volume, solution organic composition, solution drying rates and matrix/analyte co-crystallization methods. We also investigated the use of the 96-well elastomeric device for coupling MALDI-TOFMS analysis directly to high flow rate (1 mL/min) reversed-phase (rp)-HPLC. By developing an optimized, robust sample preparation protocol, we were able to obtain mass spectra with a high signal-to-noise ratio from peptide standards present at the 50-fmol level in large starting volumes of solution. PMF analyses were possible from 1-pmol and 500-fmol protein-digest standards. Coupling the device to high-flow HPLC (750 microL/min) yielded a robust and semi-automated means to obtain enhanced MALDI-TOFMS data at 500 ng of protein digest. These methodologies developed for this simple, on-target, elastomeric device show promise for streamlining the sample preparation process from HPLC to MALDI-MS.

Electrophoretic separations of cerebrospinal fluid proteins in clinical investigations

The cerebrospinal fluid (CSF) is a key sample in the research for novel molecular biomarkers of neurodegenerative disorders. CSF represents a repertoire of neuro-secreted, biosynthesised and metabolised molecular products of the central nervous system (CNS). Diffusion of macromolecules from the peripheral circulatory system to the CSF is highly regulated by the blood-brain barrier, which prevents uncontrolled distribution of proteins in the CNS. The development of reproducible high resolution separations of proteins in 2-D electrophoresis methods by the advent of immobilised pH gradient has opened the route to multivariate holistic protein pattern investigation of CSF into neurodegenerative disorders. Moreover, the introduction of pre-fractionation techniques such as free flow electrophoresis is currently increasing the dynamic depth of proteome analysis. Alzheimer's disease (AD) and other forms of dementia, demyelinating diseases, Parkinson's disease (PD), and Creutzfeldt-Jakob disease (CJD) have been evaluated for biomarker discovery by CSF investigation in multiple studies. However, the statistical design of these clinical cross-sectional investigations remains a limited factor given the strong statistical power required for complex multivariate analysis. These initial evidences are of particular interest in dissecting specific molecular mechanisms. The development of fast and economic profiling of CSF by linear matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) is providing a new ancillary technology to assess sample quality and pre-analytical requirements. In the following we take into account all these issues in the CSF proteomics investigation, especially highlighting the possible application in the development of clinical molecular biomarkers.

Clin Chem Lab Med 2007;45:437–49.

Multisample matrix-assisted laser desorption source for molecular beams of neutral peptides

We developed and tested a multisample laser desorption source for producing stable molecular beams of neutral peptides. Our apparatus is based on matrix-assisted laser desorption technique. The source consists of 96 different targets which may be scanned by a software control procedure. Examples of molecular beams of neutral peptides are presented, as well as the influence of the different source parameters on the jet.

Identification and characterization of DNA-binding proteins by mass spectrometry

Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.

Picoliter droplet formation on thin optical fiber tips

In this paper, we present experimental results on how minute droplets are formed on fiber optic end faces. Results show that reproducible picoliter volumes can be generated when fibers are retracted from an aqueous phase contained under an inert fluorinated immiscible liquid, with a coefficient of variation (CV) of 0.7-2.3%. The droplet formation was analyzed as a function of the fiber diameter, retraction speed, and wettability. Experiments reveal a volume-determining critical equilibrium contact angle between 60 degrees and 75 degrees , defining the onset of fiber end-face dewetting. The dynamics of the droplet snap-off progression was characterized using high-speed imaging in order to explain the observed wettability-volume dependency.

Recent developments in methods and technology for analysis of biological samples by MALDI-TOF-MS

Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) is widely used in a variety of fields because it has the characteristics of speed, ease of use, high sensitivity, and wide detectable mass range for obtaining molecular weights and for structural characterization of macromolecules. In this article we summarize recent developments in matrix additives, new matrices, and sample-pretreatment methods using off-probe or on-probe techniques or nanomaterials for MALDI-TOF-MS analysis of biological samples.

Microfluidic technologies for MALDI-MS in proteomics

The field of microfluidics continues to offer great promise as an enabling technology for advanced analytical tools. For biomolecular analysis, there is often a critical need to couple on-chip microfluidic sample manipulation with back-end MS. Though interfacing microfluidics to MS has been most often reported through the use of direct ESI-MS, there are compelling reasons for coupling microfluidics to MALDI-MS as an alternative to ESI-MS for both online and offline analysis. The intent of this review is to provide a summary of recent developments in the integration of microfluidic systems with MALDI-MS, with an emphasis on applications in proteomics. Key points are summarized, followed by a review of relevant technologies and a discussion of outlook for the field.

Sample Preparation for MALDI Mass Spectrometry Using an Elastomeric Device Reversibly Sealed on the MALDI Target

A new method for improving low-concentration sample recovery and reducing sample preparation steps in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is presented. In the conventional approach, samples are typically desalted and/or concentrated with various techniques and deposited on the MALDI target as small droplets. In this work, we describe a new approach in which an elastomeric device is reversibly sealed on the MALDI target to form a multi-well plate with the MALDI target as the base of the plate. The new format allows a larger volume (5-200 microL) of samples to be deposited on each spot and a series of sample handling processes, including desalting and concentrating, to be performed directly on the MALDI target. Several advantages have been observed: (i) multiple sample transferring steps are avoided; (ii) recovery of low-concentration peptides during sample preparation is improved using a novel desalting method that utilizes the hydrophobic surface of the elastomeric device; and (iii) sequence coverage of the peptide mass fingerprinting map is improved using a novel method in which proteins are immobilized on the hydrophobic surface of the elastomeric device for in-well trypsin digestion, followed by desalting and concentrating the digestion products in the same well.

Qualitative and Quantitative Analysis of Pharmaceutical Compounds by MALDI-TOF Mass Spectrometry

In this report, we discuss key issues for the successful application of MALDI-TOF mass spectrometry to quantify drugs. These include choice and preparation of matrix, nature of cationization agent, automation, and data analysis procedures. The high molecular weight matrix meso-tetrakis(pentafluorophenyl)porphyrin eliminates chemical noise in the low-mass range, a "brushing" spotting technique in combination with prestructured target plates enables fast preparation of homogeneous matrix crystals, and addition of Li+ leads to intense cationized drug species. Complex biological samples were cleaned up using a 96-well solid-phase extraction plate, and the purified samples were automatically spotted by a pipetting robot. To obtain a suitable data analysis procedure for the quantitative analysis of drugs by MALDI-TOF mass spectrometry, various data processing parameters were evaluated on our two model drugs lopinavir and ritonavir. Finally, and most importantly, it is shown that the above-described procedure can be successfully applied to quantify clinically relevant concentrations of lopinavir, an HIV protease inhibitor, in extracts of small numbers of peripheral blood mononuclear cells (1 x 10(6)).

High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

It has become evident that the mystery of life will not be deciphered just by decoding its blueprint, the genetic code. In the life and biomedical sciences, research efforts are now shifting from pure gene analysis to the analysis of all biomolecules involved in the machinery of life. One area of these postgenomic research fields is proteomics. Although proteomics, which basically encompasses the analysis of proteins, is not a new concept, it is far from being a research field that can rely on routine and large-scale analyses. At the time the term proteomics was coined, a gold-rush mentality was created, promising vast and quick riches (i.e., solutions to the immensely complex questions of life and disease). Predictably, the reality has been quite different. The complexity of proteomes and the wide variations in the abundances and chemical properties of their constituents has rendered the use of systematic analytical approaches only partially successful, and biologically meaningful results have been slow to arrive. However, to learn more about how cells and, hence, life works, it is essential to understand the proteins and their complex interactions in their native environment. This is why proteomics will be an important part of the biomedical sciences for the foreseeable future. Therefore, any advances in providing the tools that make protein analysis a more routine and large-scale business, ideally using automated and rapid analytical procedures, are highly sought after. This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry - one of the most commonly used analytical tools in proteomics - for high-throughput analyses.

Three-layer matrix/sample preparation method for MALDI MS analysis of low nanomolar protein samples

A robust and sensitive sample preparation method is presented for matrix-assisted laser desorption ionization (MALDI) mass spectrometric analysis of low nanomolar concentrations of proteins containing high amounts of common salts and buffers. This method involves the production of densely packed sub-micrometer matrix crystals by depositing a matrix solution on top of a matrix seed-layer prepared on a MALDI target. A sub-microliter aliquot of analyte solution is then directly added to the top of the matrix crystals to form a thin-layer. alpha-Cyano-4-hydroxycinnamic acid (4-HCCA) is used as matrix and demonstrated to give better performance than other commonly used matrices, such as 2,5-dihydroxybenzoic acid (DHB), 2-(4-hydroxy-phenylazo) benzoic acid (HABA), or sinapinic acid. This three-layer method is shown to be superior to the other MALDI sample preparation methods, particularly for handling low nanomolar protein solutions containing salts and buffers.

A chick retinal proteome database and differential retinal protein expressions during early ocular development

Proteomics approach as a research tool has gained popularity in a growing number of basic and clinical researches. However, proteomic research has yet to gain significant momentum in eye research. Hence, we decided to build a retinal proteome database using postnatal retinal tissue from chick, a commonly used animal model in eye research. Employing 2-D gels with the coverage of 3-10 pH gradients, we were able to resolve hundreds of proteins from young chick retinae. Among them, 155 high abundant proteins were identified by Peptide Mass Fingerprinting (PMF) after the Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS). These proteins were then classified according to their functions. Making use of the retinal database, we were able to identify several differentially expressed proteins that might be involved in early retinal development by comparing the 2-DE maps of chick retinal tissues (3, 10, and 20 days after hatching). With the current proteomics approach, we not only documented the most abundant soluble proteins in the chick retinal tissue, but also demonstrated the dynamic protein expression changes during early ocular development. This represents one of the first steps in building a complete protein database in chick retinae which is applicable to the study of eye diseases from a few selected protein candidates to the whole proteome. Proteomic technology may provide a high throughput platform for advancing eye research in the feasible future.

Phosphonoacetate hydrolase from Penicillium oxalicum: Purification and properties, phosphate starvation-independent expression, and partial sequencing

The enzyme responsible for the hydrolysis of phosphonoacetic acid, a non-biogenic C-P compound, was purified to electrophoretic homogeneity from a wild-type strain of Penicillium oxalicum. A 50-fold enrichment was obtained by a combination of anion exchange, hydrophobic interaction and MonoQ-fast protein liquid chromatography, with a yield of one-third of the initial activity. A characterization of the protein showed both similarities and differences with respect to the well-characterized bacterial counterpart. The fungal phosphonoacetate hydrolase is a 43-kDa monomeric protein showing low affinity toward its substrate and high sensitivity to even mildly acidic pH values. Enzyme activity neither required nor was stimulated by the presence of divalent cations. Polyclonal antibodies were raised in mouse against the purified protein, allowing the study of enzyme induction as a function of the phosphate status of the cell. Peptide mass mapping led to the determination of about 20% of the primary structure. Despite the biochemical differences, amino acid alignment showed a high degree of similarity of the fungal hydrolase with the few sequences available to date for the bacterial enzyme. The possible physiological role of a phosphonoacetate hydrolase is discussed.

2,5-Dihydroxyacetophenone: a matrix for highly sensitive matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis of proteins using manual and automated preparation techniques

2,5-Dihydroxyacetophenone (DHAP) is presented as a matrix which enables highly sensitive matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric analysis of peptides, proteins and glycoproteins on AnchorChip targets. Depending on the protein, lower fmol amounts can be detected due to the increased homogeneity and concentration of the crystallization of the analyte/matrix mixture on the anchors. Best results could be generated in the mass range of 8-100 kDa. All sample/matrix preparation steps starting from mixing of DHAP matrix solution with sample solution to the transfer of the mixture to the MALDI-TOF target can be performed manually or automatically allowing low- and high-throughput analyses.

Mass Spectrometric Identification of Proteins in Complex Post-Genomic Projects

The rapidly developing proteomics technologies help to advance the global understanding of physiological and cellular processes. The lifestyle of a study organism determines the type and complexity of a given proteomic project. The complexity of this study is characterized by a broad collection of pathway-specific subproteomes, reflecting the metabolic versatility as well as the regulatory potential of the aromatic-degrading, denitrifying bacterium 'Aromatoleum' sp. strain EbN1. Differences in protein profiles were determined using a gel-based approach. Protein identification was based on a progressive application of MALDI-TOF-MS, MALDI-TOF-MS/MS and LC-ESI-MS/MS. This progression was result-driven and automated by software control. The identification rate was increased by the assembly of a project-specific list of background signals that was used for internal calibration of the MS spectra, and by the combination of two search engines using a dedicated MetaScoring algorithm. In total, intelligent bioinformatics could increase the identification yield from 53 to 70% of the analyzed 5,050 gel spots; a total of 556 different proteins were identified. MS identification was highly reproducible: most proteins were identified more than twice from parallel 2DE gels with an average sequence coverage of >50% and rather restrictive score thresholds (Mascot >or=95, ProFound >or=2.2, MetaScore >or=97). The MS technologies and bioinformatics tools that were implemented and integrated to handle this complex proteomic project are presented. In addition, we describe the basic principles and current developments of the applied technologies and provide an overview over the current state of microbial proteome research.

Kinetic Energy of Free Electrons Affects MALDI Positive Ion Yield via Capture Cross-Section

A method for enhancing positive analyte ion signal in MALDI is described. The idea is based on influencing the kinetic energy of free electrons emitted from the organic/metal interface. It has been recently shown that free electrons in MALDI have energies around 1 eV. This energy is close to the maximum capture cross-section of most common MALDI matrices, leading to the efficient formation of negative matrix ions. This results in the reduction of the positive analyte ion yield. The effect can be minimized by shifting the kinetic energy of the electrons away from the maximum of the matrix capture cross-section by choosing a different substrate material.

Chemomechanical functionalization and patterning of silicon

The chemomechanical method has emerged as a straightforward and convenient tool for simultaneously functionalizing and patterning silicon. This technique simply consists of wetting (or exposing) a silicon surface to a reactive chemical and then scribing. Scribing activates the surface and leads to monolayer formation. The properties of the monolayers are dependent on the reactive chemicals used, and mixed monolayers and funtionalized monolayers are easily produced with mixed chemicals or alpha,omega-bifunctional compounds, respectively. Both micrometer and nanometer sized functionalized features have been created. It has been shown that this technique has potential in a variety of applications.