May 1, 2006 (Vol. 26, No. 9)

Customer-driven Applications Steal the Show

At the 57th &#8220Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy (Pittcon)&#8220, held recently in Orlando, the focus of new product and service launches was on meeting customers demands and adjusting to the realities of the life science market. Seamless integration of products and workflow, plug and play capability, set it and forget it runs, lower detection levels, higher-throughput, and minimizing downtime are just a sampling of the capabilities vendors added to their products.

Protein Analysis

&#8220Customers want valid answers to complex questions with high reproducibility in less time than it takes them today,&#8220 said Rick Carberrry, LC/MS senior director of marketing at Agilent Technologies ( Several additions to Agilents 6000 Series of LC/MS solutions do just that, and were among the over 60 new products and services that Agilent unveiled.

The 6340 Ion Trap LC/MS allows scientists to study proteins in a manner previously achievable only on expensive, floor-standing instruments with dedicated operators. Analysis of post-translational modifications on ion trap mass spectrometers can be challenging for protein studies, as standard ion fragmentation methods often cause labile phosphates, glycans, and other chemical modifications to disscociate from peptides. The 6340 is equipped with an electron transfer dissociation (ETD) unit, providing a softer mode of fragmentation that preserves these labile modifications.

Users can also alternate between ETD and collision-induced modes of fragmentation from scan to scan, which helps to pinpoint the precise identity and location of a chemical modification. Unlike FT-MS devices, the 6340 supports rapid nano-scale chromatography, facilitating shot-gun proteomics studies, involving the analysis of all proteins extracted from whole cell lysates.

Thermo Electron ( released several additions to its Proteomicsn suite of solutions, aimed at enhancing the potential for protein identification and quantification. According to Thermo, the LTQ Orbitrap provides an alternative to hybrid TOF systems by improving protein characterization, accelerating protein database searches, and reducing false identification rates. To achieve protein quantitation, Thermo offers Pulsed-Q Dissociation, a new fragmentation technique that eliminates the low-mass cut-off for ion traps and allows quantitation with iTRAQ labeling reagents.

Additionally, Thermos BioWorks software has been extended to facilitate the use of all major protein quantitation techniques, namely SILAC, metabolic labeling, iTRAQ, and ICAT. SEQUEST protein identifications can now be combined with quantitative data for an accurate view of protein expression levels.

The IgY-R7 Rodent and Single-Component Chemistries were added to Beckman Coulters ( family of ProteomeLab Partitioning Systems for the isolation and analysis of protein-based biomarkers. According to Beckman Coulter, the IgY-R7 Rodent Chemistry selectively partitions seven highly abundant proteins&#8212up to 70&#37 of the protein mass&#8212from rat or mouse serum or plasma. The new Single-Component kits specifically capture a choice of seven abundant plasma proteins (albumin, IgG, fibrinogen, transferrin, alpha-1-antitrypsin, haptoglobin, and IgM), enabling a more targeted approach for specific protein partitioning.

Double Your Throughput

Dionex ( launched the UltiMate 3000 series of HPLC systems for applications ranging from nanoflow proteomic analysis to semipreparative purification of small molecules. The series features seven single- and five dual-gradient systems. The UltiMate 3000 series x2 Dual-Gradient systems allow doubling throughput using tandem or parallel LC techniques. The x2 Dual-Gradient systems also automate sample preparation for matrix elimination or analyte enrichment, enabling direct injection of complex samples.

Dionex Chromeleon software helps new users overcome the entry barriers to column-switching techniques, while software panels provide single-point control. Instrument logs and audit trails document all parameters and events during analysis, facilitating method optimization and traceability of results. AutoQ instrument qualification tests automate validation of the system.

Getting More From Routine Analysis

Cerno Bioscience ( unveiled its flagship software product, MassWorks, designed to help researchers get high mass accuracy from their workhorse instruments. DirectRead technology reads most vendor data formats directly. Data files from users normal MS software is simply opened in MassWorks, reducing the possibility of transcription errors. The Calibration Wizard guides the selection and processing standard ions. After the spectra is calibrated, AccuPick peak picker locates each corrected peak.

Minimizing User Intervention

&#8220Researchers tell us that manual LC-MS/MS method development can be time consuming for analysts, considering, for example, that it may take as long as five to 10 hours to process 30 compounds,&#8220 says Iain Mylchreest, vp and general manager of life sciences mass spectrometry at Thermo Electron.

Thermos QuickQuan software for automated LC-MS/MS quantification has an automated online infusion mode and valve switching design, allowing for auto-tuning to automate quantification of chemically diverse compounds. Analytical information is stored either in Microsoft Access or Oracle databases, facilitating rapid data exchange across global networks.

Seamless Integration

In response to requests from researchers who want to harness the advantages of certain applications using UPLC with MS, Waters ( and Thermo Electron recently entered into a collaborative agreement to provide greater integration and connectivity between Waters Acquity UPLC and Thermos range of MS solutions.

&#8220UPLC peaks are narrower and sharper, signal-to-noise ratios are higher, and run times are shorter, which are all key factors in enhancing the performance of virtually any mass spectrometer, thus bringing laboratories new levels of efficiency. For Waters customers, the seamless combination of UPLC technology with Thermos high performance mass spectrometry systems promises to bring laboratories more information per unit of time resulting in greater productivity,&#8220 says Rohit Khanna, vp of worldwide marketing Waters.

Decreasing Downtime

An increasingly important customer concern is increasing system uptime and addressing issues before they occur and escalate. With this in mind, Waters extended Connections Insight, an intelligent device service platform offered as a value-added service along with its Acquity UPLC and nanoAcquity UPLC systems. Connections Insight provides users with real-time system monitoring and alert notification, predictive maintenance technology, and the ability to contact Waters directly from the Acquity system.

The offering now includes performance status reports, available automatically via monthly email, including performance and usage information for instrument counters, auto sampler injections, lamp hours, volume of solvent delivered, lamp ignition, and column usage (injections per column). With user permission, Waters support engineers can log-in and remotely diagnose system performance and operational issues in real-time, eliminating the need for an on-site engineer.

To help labs decrease the downtime of their liquid-handling equipment and ensure confidence in data, Artel ( introduced the MVS Advanced multichannel instrumentation verification platform. &#8220As liquid-handling technology continues to advance and becomes more miniaturized, new methodologies are needed to verify instrument and assay performance,&#8220 states Kirby Pilcher, president. &#8220We recognized the rapidly increasing number of laboratories working with alternative test solutions and higher density 384-well plates, characterized by minute volumes.&#8220

Fully customizable, the MVS Advanced can optimize liquid handling instrumentation with test solutions with the same viscosity as solutions used in actual assays.

Since each customer is unique, and their needs can change unpredictably from one day to the next, this customizability is a must when shopping around for any life science solution. With this in mind, Perkin Elmer ( unveiled new architecture for its latest version of Labworks LIMS. Version 5.9 provides users with a new toolkit to customize site-specific data structure and presentation utilized by the LIMS modules. By virtually eliminating the need for users to write their own custom interfaces, Labworks Lims v5.9 reduces implementation time and costs, as well as long-term cost of ownership.

&#8220Weve used the Microsoft.Net development platform to create an architecture that provides users with an unprecedented ability to custom-tailor their own systems,&#8220 says Jonathan Rennert, vp and general manager, analytical sciences, for PerkinElmers Life and Analytical Sciences division. &#8220The bottom line is that we put the customers in the drivers seat. They can easily add functionality as their needs change and evolve.&#8220

A new Data Class Designer Tool enables users to easily add and integrate customized data fields and build their own structures for information availability. The Template Designer layout tool allows the user to control how information is presented and organized, with a redesigned, integrated query mechanism that eliminates imposed hierarchies to significantly streamline data searches. &#8220You no longer need to think like a LIMS developer to query your data,&#8220 adds Rennert.

The Labworks Desktop has been redesigned to support customer-defined workflow navigation. Module folders, along with the related files, reports, and templates, are displayed in a familiar Windows format for greater ease-of-use. Users can also create multiple levels of folder sharing or designate restrictions to specific folders.

Getting the Big Picture

For customers concerned with data deluge, Bio-Rad ( enhanced its KnowItAll Informatics system to include comparative visualization, data mining, and analysis to assess the similarities and dissimilarities in massive amounts of spectral, chromatographic, or other graphical data. Overlap Density Heatmaps and Overlap Density Consensus Object displays allow visualiztion of features of overlapped objects by color coding the areas from the highest to the lowest amount of overlap.

&#8220Not being able to see the forest for the trees is an inherent problem in the traditional stacked display of spectra or chromatograms, because information content diminishes as more objects are stacked,&#8220 said Ty Abshear, Bio-Rads informatics division head of software development. &#8220Overlap Density Heatmaps reverse this situation by allowing comparative visualization of the overlap of vast numbers of spectra or chromatograms.&#8220

Traditionally, the visualization of multiple spectra or chromatograms takes place in an overlay, offset, or stacked plot. These plotting methods obliterate trends when viewing large amounts of data. The Overlap Density Heatmap and Overlap Density Consensus Spectrum technologies manage large amounts of data so that trends and other useful information can be observed. This is especially useful when considering the large amounts of graphical data associated with metabolomics, genomics, or proteomics.

Speed and Resolution

Shimadzu Scientific Instruments (SSI; designed the Prominence High-Throughput HPLC system for simultaneous speed and high resolution. The network-ready HPLC addresses high-speed requirements by providing the XR column series, 2.2-&#181m packing material columns. Shimadzu says these columns generate less backpressure compared to other commercially available sub-two micron columns, adding speed without sacrificing performance.

Also in the Prominence line of products, Shimadzu claims the SPD-20A UV detector offers fast response and sampling rates, and the SIL-20A Autosampler delivers a 10 second injection cycle with virtually no carryover.

The Prominence High-Throughput LC features stable operation at 85C, making it ideal for elevated temperature LC. Utilizing these standard components, a 23-second cycle time was achieved with gradient separations of a seven-component mixture of alkylphenones with no overlapping injections, according to the company.

&#8220In order to achieve high-throughput, not only must the run time of a single analysis be shortened, but the total cycle time of the injection sequence and run time needs to be optimized. What point is there to a 30-second analysis time, if the subsequent analysis requires 45 seconds to inject?&#8220 notes Curtis R. Campbell, Ph.D., SSIs HPLC product manager.

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