Protein identification platform utilizing micro dispensing technology interfaced to matrix-assisted laser desorption ionization time-of-flight mass spectrometry

An integrated protein microcharacterization/identification platform has been developed. The system has been designed to allow a high flexibility in order to tackle challenging analytical problems. The platform comprises a cooled microautosampler, an integrated system for microcolumn HPLC, and a capillary reversed-phase column that is interfaced to matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) system via a low internal volume flow-through microdispenser. The chromatographic separation is continuously transferred onto a MALDI target plate as discrete spots as the dispenser ejects bursts of droplets of the column effluent in a precise array pattern. A refrigerated microfraction collector was coupled to the outlet of the flow-through microdispenser enabling enrichment and re-analysis of interesting fractions. The use of target plates pre-coated with matrix simplified and increased the robustness of the system. By including a separation step prior to the MALDI-TOF-MS analysis and hereby minimizing suppression effects allowed us to obtain higher sequence coverage of proteins compared to conventional MALDI sample preparation methodology. Additionally, synthetic peptides corresponding to autophosphorylated forms of the tryptic fragment 485-496 (ALGADDSYYTAR) of tyrosine kinase ZAP-70 were identified at sensitivities reaching 150 amol.     

Ready-made matrix-assisted laser desorption/ionization target plates coated with thin matrix layer for automated sample deposition in high-density array format.

The methodology for ready-made matrix-assisted laser desorption/ionization (MALDI) target plates covered with an optimized thin layer consisting of matrix and nitrocellulose has been developed. Piezoelectric microdispensing enabled sample depositions in a high-density array format of 2000 sample depositions on a conventionally sized target plate (45 x 47 mm). The sample depositions were made reproducibly in a fully automated mode by using an in-house developed computer-controlled piezoelectric flow-through microdispenser. Additionally, the piezoelectric technique facilitated significant analyte enrichment that increased the detection sensitivity. The MS signal was obtained rapidly, generally within ten laser pulses. An airbrush device was used to generate a fine spray of matrix and nitrocellulose dissolved in acetone. The acetone evaporated instantly when reaching the target plate leaving the entire surface with a thin and uniform matrix/nitrocellulose coating consisting of very small crystals of matrix embedded in the nitrocellulose. These crystals acted as a seed-layer on subsequent analyte depositions, rendering homogeneous sample spots when using alpha-cyano-4-hydroxycinnamic acid (CHCA) as matrix. The relative standard deviation of the signal intensity between spots was (20-30)% (n = 30). The detection sensitivity was improved by restricting the sample spot diameter to 300 microm. The spot size was affected by the deposition rate and the evaporation rate of the dispensed sample volume. Mass spectra of a 25-amol peptide mixture deposition were successfully recorded.     

New aspects on the dielectric properties of the alkali halides with divalent impurities

Dielectric losses were measured in the following crystals NaCl+ (Mg²⁺, Co²⁺, Ni²⁺, Sr²⁺, Ca²⁺, Mn²⁺, Zn²⁺, Cd²⁺, Ba²⁺, Pb²⁺), KCl + (Ca²⁺, Sr²⁺, Ba²⁺, ²⁺, Pb²⁺) and KBr + (Sr²⁺, Ba²⁺) in the frequency region 5–500 kHz. It was found that when the divalent cation impurity has an electronic configuration similar to the inert gases (1) no observable deviation from simple Debye theory exists (2) the activation energy Φ increases linearly with the ionic radius of the impurity.The above observations (1) and (2) do not hold when the divalent cation impurity has d-electrons in the outer subshell.     

Chaogates: morphing logic gates that exploit dynamical patterns

Chaotic systems can yield a wide variety of patterns. Here we use this feature to generate all possible fundamental logic gate functions. This forms the basis of the design of a dynamical computing device, a chaogate, that can be rapidly morphed to become any desired logic gate. Here we review the basic concepts underlying this and present an extension of the formalism to include asymmetric logic functions.     

Data Envelopment Analysis Applied to Electricity Distribution Districts

In this paper Data Envelopment Analysis (DEA) is used to evaluate efficiency measures for the 45 distribution districts of the Greek Public Power Corporation (PPC). Results are derived under different sets of assumptions and are compared with simple productivity indices used by PPC and with efficiency measures produced by econometric methods. DEA scores appear to be more reliable than simple productivity indices. Comparison of the different cases explains the reason for the low efficiencies, which can be due to the management of controllable inputs, the design of the supply system or other environmental factors.     

A unified formulation of the machine scheduling problem

A wide class of machine scheduling problems can be formulated as ILP problems and solved by branch and bound using the out-of-kilter algorithm for the solution of the subproblems.     

Implementation of a protein profiling platform developed as an academic-pharmaceutical industry collaborative effort

As much attention has devoted to the proteome research during the last few years, biomarker discovery has become an increasingly hot area, potentially enabling the development of new assays for diagnosis and prognosis of severe diseases. This is the field of research interest where efforts originating from both academic and industrial groups should jointly work on solutions. In this paper, we would like to demonstrate the fruitful combination of both research domains where the scientific crossroads sprout fresh ideas from the basic research domain and how these are refined and tethered to industrial standards. We will present an approach that is based on novel microfluidic devices, utilizing their benefits in processing small-volume samples. Our biomarker discovery strategy, built around this platform, involves optimized samples processing (based on SPE and sample enrichment) and fast MALDI-MS readout. The identification of novel biomarkers at low-abundance level has been achieved by the utilization of a miniaturized sample handling platform, which offers clean-up and enrichment of proteins in one step. Complete automation has been realized in the form of a unique robotic instrumentation that is able to extract and transfer 96 samples onto standard MALDI target plates with high throughput. The developed platform was operated with a 60 sample turnaround per hour allowing sensitivities in femtomol regions of medium- and low-abundant target proteins from clinical studies on samples of multiple sclerosis and gastroesophageal reflux disease. Several proteins have been identified as new biomarkers from cerebrospinal fluid and esophagus epithelial cells.     

Is Multidimensional High Performance Liquid Chromatography (HPLC) an Alternative in Protein Analysis to 2D Gel Electrophoresis?

The interactive modes of High Performance Liquid Chromatography (HPLC) of proteins provide a platform for the construction of a multidimensional HPLC system coupled to mass spectrometry. We present a system composed of both anion and cation exchanger columns, in the first dimension, and n‐octadecyl bonded 1.5 μm nonporous silica columns in the second dimension. Both columns are operated under gradient conditions. A system suitability test with standard proteins showed that the total analysis can be performed within about 20 minutes. The fractions taken from the ion exchanger column are directly analyzed within one minute on the reversed phase column at a high flow rate. Two reversed phase columns are applied and operated alternatively: while the first column performs the separation within one minute, the analytes leaving the first dimension are enriched in an on‐column focusing mode on top of the second column. The sample clean‐up and enrichment is performed on a novel type of restricted access cation exchanger column with internal sulfonic acid groups and external diol groups. The columns exhibit a molecular weight exclusion limit for globular proteins of about 15 kDa. Our next studies will be directed towards the analysis of proteins and peptides from extracts of fibroblasts.