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Software solutions handle data from different vendors

8th June 2015

Posted By Paul Boughton


The new portal delivers streamlined software solutions

Growing end-user demand for interface simplicity and seamless deployment is driving software solutions that can handle data from many different spectroscopy techniques. Sean Ottewell reports

As laboratories strive to reduce costs and boost efficiency, the focus is turning to software solutions that can interpret results from different vendors.

For example, the latest launch from cheminformatics specialist Advanced Chemistry Development (ACD/Labs) is a web-enabled portal to extend its ACD/Spectrus analytical and chemical intelligence platform.

The portal is being launched through a series a domain-specific market applications. The first, ACD/Labs' Open Access solution, is targeted towards delivering streamlined results to open access or walk-up laboratory environments.

Open Access combines the web-enabled ACD/Spectrus Portal with its established automation technology and workflow components. Sophisticated data processing and analysis algorithms deliver interpreted NMR and LC/MS results from a variety of different instrument vendors in what the company says is the industry's first web-based NMR and LC/UV/MS review panel. Chemists rely on this information to determine the identity and purity of their samples and to make quick decisions about the fate of their reactions.

ACD/Labs already counts companies such as Hoffmann-LaRoche, Bayer Crop Science, GSK, and AstraZeneca as users of its spectroscopy processing and prediction tools. However, the demand for one software application to cover many technologies has driven the latest development.

David Hardy, MS product manager, explains: “With increased usage, we met many demands for better interpretation tools, specifically around LC/UV/MS data. We have always focused on leveraging our chemically intelligent algorithms to deliver answers instead of just data. Providing these answers via a browser-based interface, with the ACD/Spectrus Portal, was the logical next place to go."

Vendor-neutral solution

The company is keen to help analytical laboratories to become more agile in their instrument selection and retention processes. Its vendor-neutral solution means that users can reduce the costs of running sets of different instruments, software support and training. The idea here is to free up scientific organisations to choose the instrumentation that works best for their needs, and to bring all the data into one easy to use and deploy interface.

New from AB Sciex, and aimed at research rather than diagnostic procedures, is ProteinPilot software. Again, ease of use is the most important feature and ProteinPilot streamlines protein identification and quantitation, enabling users to identify hundreds of peptide modifications and non-tryptic cleavages simultaneously. It enables users to easily distinguish protein isoforms, protein subsets, and suppress false positives, as well as visualise peptide-protein associations and relationships. With generic input for non-SCIEX instruments, the software is compatible with all proteomics MS/MS systems.

As such, the software enables extensive automatic peptide identification so users can search for hundreds of biological and other modifications, genetic variants, and unexpected cleavages simultaneously with the Paragon Algorithm, without an explosion of false positives, cost in expanded search time, or the complexity of multi-stage analyses that plague alternate approaches. A single click triggers complete data processing (including signal processing) to make peak lists and integrate signals for quantitation, peptide identification (including data re-calibration), protein inference of identified peptides, and analysis of relative quantitation for label-based workflows.

Protein isoform and protein subset differentiation, as well as false positives supression is enabled using the embeddedPro Group Algorithm for protein-grouping analysis. The novel user-interface allows sample information to be entered based on terms used by laboratory scientists, and the software intelligently determines the search parameters.

AB Sciex says the result of these innovations is that top-quality identification results are delivered without the need for informatics expertise – and that third party software vendors can easily integrate it with their own products.

Also aimed at automating the processing and interpretation of product LC/MS data, in this case associated with biopharmaceuticals, is BiopharmaLynx from Waters. The software automatically processes mass MS data, including peptide map results and intact mass measurements. Similarly, it automatically analyses and assigns results, defines the sequence and features of known proteins and determines the identity of modified forms. Users can edit assignments, annotate new peaks and compare experimental samples with a reference using visualisation and tabular tools. In terms of intact proteins, BiopharmaLynx lets users define deconvolution settings for known proteins and as generic for unknown proteins. It also automatically calculates percentages of each protein variant.

In an effort to simplify interaction with MS systems and increase laboratory productivity, the company also offers MassLynx spectrometry software. With an intuitive interface and intelligent sample control, MassLynx is focused on delivering the versatility and flexibility demanded by laboratories today. It achieves this via easy to use application managers that allow users to really focus the power of mass spectrometry on specific laboratory tasks.

Finally, Agilent deconvolution reporting software (DRS) for GC/MS is an application for target compound analyses that combines results from the Agilent MSD Productivity ChemStation, the US National Institute of Standards and Technology (NIST) Automated Mass Spectral Deconvolution and Identification Software (AMDIS), and the NIST 2008 Mass Spectral Search Programme (NIST08) into one easy-to-read report. DRS works with any Agilent RTL Database Library and can work with full-scan or SIM data.

Agilent says the software can take as little as one minute per sample of processing time, works especially well with dirty matrices, and is more thorough than standard quantification and library search methods.

Target screening and data mining

TargetView from Markes International is aimed at GC-MS analysts who need to rapidly screen chromatograms against compound libraries. It is especially useful if looking for trace-level analytes apparently lost in acomplex background, or hidden under co-eluting peaks.

The company says that TargetView is special because it provides extensive GC–MS data-mining functionality, while being far less complicated and much easier to learn than other software platforms. Also, the advanced algorithms used by TargetView work behind the scenes; users don’t need to understand the detail of how it operates, or to be an expert at chemometrics, in order to get accurate, reliable results.

TargetView’s interface allows users to delve into the results as much as they want – from a simple ‘yes/no’ confirmation that a particular compound is present, to detailed examination of elution profiles, comparison of mass spectra, and generation of extracted-ion chromatograms.

Other benefits to the GC-MS analyst include identification of target compounds and unknowns, rapid screening of chromatograms against compound libraries, easy import of spectra, rapid creation of spectral libraries from various sources, suitability for all GC-MS applications, and deconvolution of co-eluting compounds.

Meanwhile, compatible with all its quantitative GC and LC mass spectrometry platforms, along with non-mass spectrometer detectors, Thermo Scientific’s TraceFinder software offers one, easy-to-use solution for laboratories performing routine analysis.

TraceFinder is designed to make routine quantitation and target analysis simple, fast and productive. The software offers a simplified workflow-driven method setup with fully automated data acquisition, data processing and reporting. Its main features include intelligent sequencing, semi-quantitative workflows and multi-peak review capabilities.





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