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Flexibility and speedy data analysis key for omics technologies

4th March 2013


Large scale proteomics and metabolomics projects rely on high-speed data analysis software, together with fast throughput analysis systems. Sean Ottewell reports on the latest developments.

AB SCIEX has launched its new Eksigent ekspert nanoLC 400 system, the world's first plug-and-play liquid chromatography (LC) system that integrates nano LC and micro LC on the same platform. As such it provides the broadest functionality with the benefits of both flow rate ranges. This flexibility enables fast and easy switching between high-sensitivity discovery proteomics and the high-throughput targeted peptide quantitation commonly used in advanced biological studies.

Discovery proteomics is a strategy in which an LC system in combination with a mass spectrometer is used to identify and quantify proteins in a global untargeted manner. Once a set of interesting proteins has been identified, targeted techniques are used to verify and validate the results in further sample types by targeted peptide quantitation. The ultimate goal is to advance the understanding of systems biology by identifying new biomarkers or new proteins of interest and to potentially improve medical methodologies.

The new Eksigent ekspert nanoLC 400 system improves the efficiency of these proteomics workflows by providing the highest separation quality and reliability.

The novel, interchangeable LC flow modules in the nanoLC 400 system allow scientists to quickly go from low flow nano LC to a higher flow rate of micro LC, with a simple switch of a module. This is ideal for mixing non-targeted and targeted approaches, especially when used with a next-generation mass spectrometer such as the AB SCIEX TripleTOF 5600+ system. In addition, the retention time stability afforded by advances in microfluidic flow control (MFCPlus technology) is critical for quantitative applications such as Scheduled MRMHR Workflow and SWATH Acquisition.

"Scientists want to do more with less," said Remco van Soest, product manager for the ekspert nanoLC 400 system at AB SCIEX. "Because the new ekspert nanoLC 400 system bridges the gap between low flow and higher flow rates in LC/MS workflows, laboratories no longer need separate LC systems to go from discovery to verification and validation in the protein biomarker research continuum. The plug-and-play functionality of the nanoLC system opens up new possibilities for biomedical and proteomics researchers."

According to van Soest, the nanoLC 400 system is the only low-flow system that - when combined with the existing Eksigent cHiPLC system - enables highly reproducible proteomics across a broad range of workflows in busy multi-user, multi-instrument laboratories. The cHiPLC system is a chip-based platform that serves as a 'docking station' for easy switching between different types of experiments, such as direct injection and trap-loading. With the new nanoLC 400 system, injections can now be done 5-10 times faster with a higher precision autosampler for nano LC.

"The Eksigent nanoLC system enables me to go to a higher flow rate within the same system, when I need it, and that is a tremendous benefit," said Nick Morrice, group leader at the Beatston Institute for Cancer Research in Glasgow, Scotland. "Nano LC with 75µm ID columns is great for thorough, detailed discovery, but it takes longer than I would like. Using microflow LC on my TripleTOF 5600 system with the 25µm ID hybrid electrode and the DuoSpray Source, my routine protein identifications using the same injection volume are three times faster than nano LC. The flexibility of being able to switch between nano LC and micro LC in minutes is really valuable. It's a step forward for the proteomics community."

Meanwhile, Scientists using Qlucore's recently-released Omics Explorer 2.3 bioinformatics software are reporting key benefits including greater ease of use and enhanced creative reporting capabilities.

"Qlucore Omics Explorer is adding more creativity to our research than any other software I have used," reported David Gisselsson Nord, associate professor in the department of clinical genetics at Lund University. "The new flexibility and wide range of plot types, introduced in Qlucore Omics Explorer 2.3, make it a lot easier to generate pictures for publications."

Previous versions of Qlucore's visualisation software have helped scientists across the globe to speed up their research projects and present their findings in areas including human diseases such as leukemia and diabetes, animal testing for allergens, and blood doping in sports.

The new version also has an advanced ability to import and export data from a wide range of devices and platforms, while enhanced presentation capabilities are enabling researchers to be much more creative when presenting findings in reports and presentations (Fig. 1).

Added features with the latest version include new box plots, line plots and histogram plots. These have been developed to help researchers visualise, explore and analyse an even wider range of integrated high-dimensional data sets interactively and in real time. With instant and simultaneous access to an even larger set of multiple plots, enhanced and faster integration and more flexible options for ordering and visualising larger heatmaps that use less memory, researchers are able to improve workflows and spend more time on testing theories and alternative hypothesis.

"It's excellent to receive such positive feedback for Qlucore Omics Explorer 2.3 so soon after its release. It has been designed by scientists with scientists needs in mind, so we were confident it would be well received, but we're pleased to hear that it's already making a significant difference to our customers," says Carl-Johan Ivarsson, president, Qlucore. "All the new features and enhancements target the same key objective: to make it simpler and faster for researchers, biologists and scientists to import, analyse and report on their own, and other, data instantly and far more creatively than they could previously with other bioinformatics software (Fig. 2)."

Research project

Qlucore started as a collaborative research project at Lund University, Sweden, supported by researchers at the departments of mathematics and clinical genetics, in order to address the vast amount of high-dimensional data generated with microarray gene expression analysis. As a result, it was recognised that an interactive scientific software tool was needed to conceptualise the ideas evolving from the research collaboration.

For its part, Agilent Technologies has entered into a co-marketing agreement with MRM Proteomics, a leading provider of advanced protein quantitation, biomarker and proteomic services to the pharmaceutical, biotechnology and diagnostics industries. The agreement will allow both organisations to offer a more complete solution, including kits, hardware and software for proteomics.

"MRM Proteomics is recognised as a pioneer and leading company in the development of mass spec based methods for protein quantification using multiple reaction monitoring," said Steve Fischer, Agilent marketing manager, metabolomics and proteomics. "The agreement is a further reflection of Agilent's continued commitment and investment in quantitative proteomics."

MRM Proteomics specialises in the highly multiplexed absolute quantitation of proteins in complex biological samples such as blood, cerebrospinal fluid and urine through MRM-MS using isotopically labelled internal standards. MRM Proteomics' workflows utilise minimal sample volumes (20µl) and according to the company are capable of unparalleled specificity and sensitivity, without the need for depletion of high-abundance proteins.

Finally, Waters Corporation and Nonlinear Dynamics have entered into an agreement to co-develop a new analytical solution that derives information from complex data sets generated by large-scale proteomics and metabolomics experiments. The two have already collaborated on the development of the Waters Omics Research Platform with TransOmics informatics, which was launched in May.

"The complexity of biological samples is so great that the sensitivity and specificity of analytical techniques required for biological discovery presents scientists with significant challenges when it comes to managing experimental data," said James Langridge, director of pharmaceutical & life sciences discovery, Waters Division. "We believe that through our partnership with Nonlinear Dynamics we can address this situation and advance the pace of discovery."

Decreasing procedural errors

PerkinElmer has launched Ensemble for QA/QC, an integrated informatics solution tailored to decrease procedural errors and accelerate data review and results delivery of quality assurance (QA) and quality control (QC) laboratories.

The solution can be implemented in virtually any industry where testing and results are needed to control manufacturing processes and to ensure the quality of raw materials, in process samples and finished goods. Some of the key industries currently served include pharmaceutical, food and beverage, chemical/petrochemical and environmental.

In QA/QC laboratories, time is of the essence, accuracy is critical and processes and procedures must be carried out and fully documented in a manner that supports regulatory compliance. The Ensemble for QA/QC platform integrates people, procedures and lab systems into one cohesive system that makes data and information available and accessible, wherever and whenever it is needed. This enables real time control and automation that helps laboratories decrease procedural errors, reduce time spent on data review and speed up the delivery of results to end users.

"Decision makers in QA/QC laboratories need critical information to respond quickly and effectively to support business decisions," said Michael Stapleton, general manager, informatics, PerkinElmer. "The new Ensemble platform enables QA/QC laboratories to maintain high attention to detail while reducing time and cost required to qualify an area or material for use, as well as deliver metrics on operational effectiveness and reduce non-value add tasks."

The platform utilises a scalable architecture to support all levels of deployment from a single site to the entire enterprise.






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