Proteomic sample preparation by microdialysis: easy, speedy, and nonselective.

Microdialysis tools have been developed for parallelized medium exchange designated for sample volumes from 10 to 100 µl, compatible with the microplate format, and guaranteeing maximum recoveries without selectivity. These tools are applicable to both protein and peptide analysis. Moreover, they may be used for binding studies as well as for reconcentration and as unique sample containers for complex operating sequences allowing contemporaneous processing and high throughput.

Long-term serum proteomes are quite similar under high- and low-flux hemodialysis treatment.

PURPOSE: Aim of the study was to identify long-term differences of middle and high-molecular-weight serum constituents under high- and low-flux hemodialysis treatments. Thus, the entire predialytic serum proteomes had to be analyzed using identical hemodialysis membrane material but with different cut-off values. METHODS AND RESULTS: A cross-over study and a global native chromatographic proteomic approach were used to analyze serum compositions of 16 patients suffering from end-stage renal disease. RESULTS: No significant or reproducible differences were found between predialytic serum samples from high- and low-flux dialysis treatments using UV-absorbance and fluorescence spectrometry, PMF, or sequence tags. In contrast, there are characteristic differences in the predialytic serum composition of the patients considered and two control sets, which include samples obtained post-dialytically from patients and samples from healthy controls. Only a fraction of ß(2)-microglobulin, an example of so-called middle molecules, exhibits the expected molecular weight. A small fraction was found with high molecular weight unaffected by any dialysis treatment. Moreover, immunoreactivity of fragments of ß(2)-microglobulin, surprisingly, was also not affected by the cut-off of dialysis membranes. CONCLUSIONS AND CLINICAL RELEVANCE: Thus, simply increasing the pore size of a hemodialysis membrane may not have any long-term effect on serum composition.

Spinal antinociceptive effects of cyclooxygenase inhibition during inflammation: Involvement of prostaglandins and endocannabinoids.

Both cyclooxygenase-1 and -2 are expressed in the spinal cord, and the spinal COX product prostaglandin E(2) (PGE(2)) contributes to the generation of central sensitization upon peripheral inflammation. Vice versa spinal COX inhibition is considered an important mechanism of antihyperalgesic pain treatment. Recently, however, COX-2 was shown to be also involved in the metabolism of endocannabinoids. Because endocannabinoids can have analgesic actions it is conceivable that inhibition of spinal COX produces analgesia not only by inhibition of PG synthesis but also by inhibition of endocannabinoid breakdown. In the present study, we recorded from spinal cord neurons with input from the inflamed knee joint and we measured the spinal release of PGE(2) and the endocannabinoid 2-arachidonoyl glycerol (2-AG) in vivo, using the same stimulation procedures. COX inhibitors were applied spinally. Selective COX-1, selective COX-2 and non-selective COX inhibitors attenuated the generation of spinal hyperexcitability when applied before and during development of inflammation but, when inflammation and spinal hyperexcitability were established, only selective COX-2 inhibitors reversed spinal hyperexcitability. During established inflammation all COX inhibitors reduced release of spinal PGE(2) almost equally but only the COX-2 inhibitor prevented breakdown of 2-AG. The reversal of spinal hyperexcitability by COX-2 inhibitors was prevented or partially reversed by AM-251, an antagonist at the cannabinoid-1 receptor. We conclude that inhibition of spinal COX-2 not only reduces PG production but also endocannabinoid breakdown and provide evidence that reversal of inflammation-evoked spinal hyperexcitability by COX-2 inhibitors is more related to endocannabinoidergic mechanisms than to inhibition of spinal PG synthesis.

Extended FMRFamides in dipteran insects: conservative expression in the neuroendocrine system is accompanied by rapid sequence evolution.

Extended FMRFamides are found throughout the central nervous system (CNS) of insects and exhibit diverse physiological effects on different target organs, such as muscles, intestine, and the nervous system. The genes encoding for extended FMRFamides are known from a number of flies, including Drosophila species, and the pest insects Lucilia cuprina, Calliphora vomitoria, and Musca domestica. No data, however, exist about the expression of the numerous paralogs of the latter three species, and studies on Drosophila melanogaster resulted in controversial findings. We could unambiguously verify, that all predictable products of the extended FMRFamide precursor are expressed in neurohemal tissues of the thoracic neuromers of these flies and can easily be identified and also sequenced by using single specimens. In addition to the confirmation of extended FMRFamides in species with known precursor sequences, the current knowledge about homologous peptides of Sarcophaga (=Neobellieria) bullata could be extended by de novo sequencing using tandem mass spectrometry. The most intriguing finding in this study was the detection of an internal gene duplication, followed by an amino acid substitution, in an insecticide-resistant strain of L. cuprina. To our knowledge, this is the first detection of such an intraspecific event and confirms the low conservation of the extended FMRFamide gene sequences. In insects, no other neuropeptide family is known that shows such sequence variability between related species.

Searching biomarker candidates in serum using multidimensional native chromatography. II Method evaluation with Alport syndrome and severe inflammation.

Biomarker search using multidimensional native liquid fractionation of serum in microplates was evaluated. From different donors, homologous sample fractions with UV absorbance depending on state of illness were selected, and their constituents were identified and quantitated by MS. Analysis of sera of patients with Alport syndrome and severe inflammation proved the reliability of the method by confirming characteristic alterations. Moreover, 23 new marker candidates were detected for Alport syndrome, some of them being involved in matrix degradation and repair, and 33 new candidates for severe inflammation, among them alpha1B-glycoprotein cysteine-rich secretory protein and an apparently low molecular-weight albumin variant.

Searching biomarker candidates in serum using multidimensional native chromatography. I. Enhanced separation method.

The microplate-based method developed by our group for non-denaturing multidimensional proteome separation was improved on using improved column arrays and a newly developed robot. Currently size exclusion, anion exchange and lectin affinity chromatography are combined orthogonally. Different samples run simultaneously to enhance reliability of intercomparison. LC-ESI (electro-spray ionization) MS/MS analysis of selected fractions identified 32,288 peptides matching 2,669 serum proteins. The present contribution (I) shows the characteristics of the method, whereas "prove of principle" by applying it to search for biomarker candidates with model diseases is reported in an accompanying paper (II).

Multidimensional chromatography: validation and efficient fishing for biomarkers and fractions containing them using the VisualCockpit software package.

2-D native LC yields thousands of fractions especially when applied to sera of different origin. Checking reproducibility of repeated separation of the same serum or searching for biomarker candidates and fractions containing them requires finding, selection, and comparison of interesting data subsets out of huge data volumes. An innovative software package is applied that markedly enhances simplicity, velocity, and reliability of (i) check of reproducibility of the separation method and (ii) analysis of proteomes pertaining to different disease states.

Robust protein quantitation in chromatographic fractions using MALDI-MS of tryptic peptides.

A method is introduced to evaluate protein concentrations using the height sum of all MALDI-MS peaks that unambiguously match theoretic tryptic peptide masses of the protein sought after. The method uses native chromatographic protein fractionation prior to digestion but does not require any depletion, labeling, derivatization, or preparation of a compound similar to the analyte. All peak heights of tryptic peptides are normalized with the peak height of a unique standard peptide added to the MALDI-MS samples. The sum of normalized peak heights, S(n), or the normalized mean peak height, M(n), reflects the concentration of the respective protein. For fractions containing various proteins, S(n) and M(n) can be used to compare concentrations of a protein between different fractions. For fractions with one predominating protein, they can be used to estimate concentration ratios between fractions, or to quantify the fractional protein concentration after calibration with pure protein solutions. Initial native fractionation retains the possibility to apply all conventional analytic procedures. Moreover, it renders the method relatively robust to MS mass accuracy. The method was validated with albumin, transferrin, alpha1-antitrypsin, and immunoglobulin G within highly complex chromatographic fractions of pathological and normal sera, which contained the respective intact native protein in dominating as well as minor concentrations. The correlation found between S(n) and the protein concentration as determined with ELISA showed that the method can be applied to select markers for distinguishing between normal and pathological serum samples.

Multidimensional proteomics of human serum using parallel chromatography of native constituents and microplate technology.

A versatile, multidimensional, and non-denaturing proteome separation procedure using microplate technology is presented, yielding a digitized image of proteome composition. In the first dimension, the sample under study is separated into 96 fractions by size exclusion chromatography (SEC). In the second dimension, the fractions of the first dimension are transferred by the liquid-handling device CyBi-Well (CyBio AG, Jena, Germany) to 96 parallel anion exchange chromatography columns. In this way the proteins are conserved in their native states and are distributed in 2400 liquid fractions with high recovery rates and sufficient reproducibility. The resulting fractions are subjected to protein quantitation and identification. Spectrophotometrical and immunological methods and enzyme activity measurements are used for quantitation. To identify proteins, the fractions are subjected to MALDI-MS, and their tryptic digests to both MALDI- and LC-ESI-MS/MS. All preparation steps except the first are applied in parallel to sets of multiples of 96 samples. The procedure may be refined by adding more separation steps and may be adapted to various protein amounts and to various proteomes. Moreover, the method offers the opportunity to investigate functional protein complexes. The method was applied to separate the normal human serum proteome. Within 255 fractions exhibiting the highest protein concentrations, 742 proteins were identified by LC-ESI-MS/MS peptide sequence tags.

UV measurements in microplates suitable for high-throughput protein determination.

An UV spectrophotometric method for protein determination using microplates is described. Using the SPECTRAmax PLUS reader, the UVStar 96- and 384-well microplates and a 96 or 384 parallel channel liquid handling technique, large-scale determinations can be performed with intraassay precision better than 3% CV (coefficient of variation) in the range from 1 to 8000 microg of protein/ml, measuring at 205, 215, and 280 nm and using different volume-dependent light-path lengths. Since the absorbance coefficient at 205 nm is found to be 30 ml/(mgxcm) for eight different proteins with a CV of 5.6% only with the Path Check option of the reader, protein concentration can be determined without any individual calibration. Samples in the volume range of 60-250 microl can be analyzed without time-consuming and expensive treatment and without sample loss. Using a special 96 or 384 parallel dialyzing device, low molecular weight substances which interfere with the analysis by their UV absorbance, such as buffers and detergents, can effectively be removed. Application examples for serum protein separation are also shown in the presence of the strongly UV absorbing detergent Triton X-100.