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The Ongoing Collaboration Aims to Exploit the High Throughput, Robustness and Ease of Use of MALDI-TOF Instruments

At the 12th HUPO World Congress, Bruker Corporation (NASDAQ: BRKR) recently announced the start of a second-phase collaboration agreement with SISCAPA Assays Technologies, Inc. (SAT). The ongoing collaboration aims to exploit the high throughput, robustness and ease of use of MALDI-TOF instruments as an alternative to nano-LC-MS technology currently used in many SISCAPA assays.

AB SCIEX Proteomics Scientist Wins HUPO 2013 Science and Technology Award

The Human Proteome Organization (HUPO) recently awarded Christie Hunter, Ph.D, director of proteomics applications at AB SCIEX, its 2013 Science and Technology Award at an award ceremony during last week’s HUPO 2013 conference in Japan. Dr. Hunter was recognized for her contributions to the development and commercialization of a breakthrough approach for targeted proteomics. The analytical strategy of targeted proteomics was recently named “Method of the Year” by Nature Methods.

Targeted proteomics is a standardized, biological research workflow that focuses on reproducibly quantifying a specific subset of proteins within a sample. It generates data that is vital for biologists to answer hypothesis-driven, biological questions.

A decade ago, proteomics research was dominated by discovery workflows, which provided valuable information on a single sample but lacked the reproducibility to generate robust quantitation across a larger sample set. New innovation was needed at the time to move the field beyond simply producing large lists of identified proteins and toward providing highly quantitative answers.

This led to the development of a multiple reaction monitoring (MRM)-triggered, tandem mass spectrometry (MS/MS) workflow at AB SCIEX to rapidly create high sensitivity MRM assays to target peptides that are unique to their associated proteins. This workflow was made possible by the combination of triple quadrupole and linear ion trap functionality in a single system called the AB SCIEX QTRAP® System.

Dr. Hunter ‒ in collaboration with researcher Dr. Leigh Anderson, the founder of the Plasma Proteome Institute and head of SISCAPA Assay Technologies ‒ pioneered a workflow that applied MRM to the targeted quantification of proteins and peptides in plasma by mass spectrometry. In their initial publication[1], Dr. Hunter and Dr. Anderson demonstrated that a targeted workflow could be applied to multiplexed quantitation of proteins in human plasma with high reproducibility and high confidence in the results.

The impact of the paper resulted in broad adoption of the MRM technique around the world to accelerate the verification and validation of putative protein biomarkers, generating more than 800 citations, according to Google Scholar. Less than a decade after this important work, most proteomics laboratories today use a triple quadrupole-based mass spectrometer to perform MRM analysis.

“We congratulate Dr. Christie Hunter on receiving such a prestigious award from HUPO in recognition of her significant contributions to the rise of targeted proteomics as a viable technique to advance biomarker research,” said Dave Hicks, Vice President and General Manager of the Pharmaceutical and Academic Business at AB SCIEX.

“Dr. Hunter and her AB SCIEX colleagues continue to participate in exciting collaborations with leading proteomics researchers around the world to drive new innovations in software, chemistries and instrumentation that further expand quantitative proteomics workflows for the growing community of mass spectrometry users at large,” added Hicks.

Currently, Dr. Hunter is playing a pivotal role in the development of higher specificity workflows for targeted protein quantitation to overcome situations where sensitivity is limited by interferences or background. She is involved in the investigation of the utility of differential mobility separations for added selectivity of quantitation of peptides in complex mixtures. She is also working to enhance data-independent acquisition strategies, such as SWATHTM Acquisition, for quantitative proteomics to increase the multiplexing and reproducibility that can be achieved in a single experiment.

Source: AB SCIEX

Key Assay Development at HUPO

Proteome Sciences presented novel data and key assay developments at the HUPO 12th Annual World Congress in Japan covering Tau in Alzheimer’s disease, SysQuant® in pancreatic cancer and a missing isoform in sugar structures of clusterin, a plasma protein biomarker for Alzheimer’s in brain atrophy.

pTau

The new Tau phosphorylation assay (pTau SRM) demonstrated powerful sensitivity and reproductivity measuring Tau phosphorylation on human and mouse models of Alzheimer’s disease from a much smaller sample amount.

In a different application the pTau SRM was successfully used to determine the effect of Tau kinase inhibitors PS110 and PS278-05 on CK1d on the Tau protein in a mouse model of Alzheimer’s. The results confirmed that Tau phosphorylation was reduced by the two compounds but not affected by the control substance.

SysQuant®

Over 5,000 different phosphorylation sites were quantified in tumour and healthy tissue in pancreas cancer with SysQuant®. In addition to major alterations in proteins related to cell morphology and motility, individual patterns of pathway activation were able to accurately predict the likelihood of tumour recurrence and to provide a truly personalised treatment regime.

Glycopreotomics

Novel data was presented that showed diagnostic changes in sugar structures attached to clusterin, a plasma marker for Alzheimer’s in brain atrophy. This revealed a unique isoform that lacked a specific branching pattern in patients with high levels of brain atrophy.

Commenting from Yokohama, Dr. Ian Pike, Chief Operating Officer, said: 

“We were delighted to be invited to the 12th HUPO congress to show results from the powerful biomarker services platform that we have developed from our TMT® mass tags for customers where we are at the forefront in proteomics. New assays for pTau and clusterin glycoprotein provide important additions to the range of assays and services that we offer our customers in Alzheimer’s The added power delivered by SysQuant® identifies thousands of phosphorylation sites across key signalling pathways that give clinicians the ability for the first time to provide real time patient management, in this case in pancreas cancer. These are exciting developments from proteomics that are fundamentally changing how clinicians identify and manage disease.”

Source: Proteome Sciences

Proteome Sciences Announces $2.1m Contract with Thermo Fisher Scientific

Proteome Sciences recently announced its largest contract to date, a technology agreement with Thermo Fisher Scientific, valued at $2.1million by Proteome Sciences, to develop advanced methods to profile changes in key cancer pathways. Proteome Sciences will provide Thermo Fisher with access to its patents covering a three-stage mass spectrometry (MS3) fragmentation methodology to deliver significantly improved analysis and accuracy. Proteome Sciences will receive cash and Thermo Fisher will provide a no-cost lease for mass spectrometry equipment for Proteome Sciences to develop the pathway assays. In addition Proteome Sciences will continue to develop advanced 20 and 30-plex Tandem Mass Tags (TMT®) for Thermo Fisher for the next additions to the TMT® range of tags.

The new MS3 TMT® (three-stage MS Tandem Mass Tag) mass spectrometry technique is a breakthrough mass spectrometry based workflow, enabling mass spectrometers to determine relative quantitation of proteins in multiple samples simultaneously and with improved accuracy.
“We are at a critical juncture toward the development of personalised medicine which requires high-resolution maps of the protein networks regulating disease,” said Dr. Ian Pike, Chief Operating Officer at Proteome Sciences. “The combination of the highest sample multiplexing rates from TMT with the industry-leading Thermo Scientific Orbitrap mass spectrometer enables us to provide an unrivalled platform to investigate subtle but significant changes in the proteome.”
Proteome Sciences will leverage the combined power of TMT® and Orbitrap® technology to develop an expanded range of mass spectrometry assays for the pharmaceutical industry. Through its SysQuant® workflows, Proteome will profile the low-level changes in activity of key cancer signalling pathways to facilitate optimal drug selection across a range of solid tumours. This will enable clinicians to provide real-time patient management and the ability, for the first time, to deliver truly personalised medicine.

“Life sciences researchers today need to perform high-quality relative quantitation of many samples quickly,” said Ian Jardine, Chief Technology Officer, Chromatography and Mass Spectrometry, Thermo Fisher Scientific. “MS3 TMT® technology greatly improves quantitative accuracy and throughput, while Orbitrap® technology dramatically increases depth and quality of data. This agreement offers customers a new paradigm in proteomics research.”
“Our agreement with Thermo Fisher sets a new benchmark to establish and apply novel diagnostic and prognostic strategies in healthcare management,” said Christopher Pearce, Chief Executive of Proteome Sciences. “It has long been our goal to provide clinicians the tools they need to provide early diagnosis of disease and better match molecular targeting medicines to the most likely responders. The output from this agreement should have a profound positive impact on the lives of large numbers of patients suffering from chronic diseases and, at the same time, provide considerable economic benefits to the health care system.”

Source: Proteome Sciences

SAP and Technical University Munich Decode Human Proteome and Make Data Available for Biomedical Research

SAP AG (NYSE: SAP) and Technical University Munich (TUM) recently announced ProteomicsDB, a new offering based on the SAP HANA® platform that stores protein and peptide identifications from mass spectrometry-based experiments. The proteomic data assembled in the new offering resulted in the identification of proteins mapping to over 18,000 human genes. This represents 90 percent coverage of the human proteome. Data stored and analyzed within ProteomicsDB can be used in basic and biomedical research for discovering therapeutic targets and developing new drugs as well as enhanced diagnosis methods.

As personalized medicine is on the rise, the healthcare field is discovering the opportunities of big data analysis. The result of a joint project between the TUM Chair of Proteomics and Bioanalytics, SAP and the SAP Innovation Center, ProteomicsDB is a major step forward in human proteomics. It currently contains more than 11,000 datasets from human cancer cell lines, tissues and body fluids and enables real-time analysis of this highly dimensional data and creates instant value by allowing to test analytical hypothesis.

ProteomicsDB is based on the SAP HANA for rapid data mining and visualization. It has been built to enable public sharing of mass spectrometry-based proteomic datasets as well as to allow users to access and review data prior to publication. The database is backed with 50 TB of storage, 2 TB RAM and 160 processing units. A direct interface to the programming languages L, C++ and R allows more flexible calculations than are possible with standard SQL. The Web interface is built on a JavaScript framework for HTML5 and optimized for Google Chrome but also available under Internet Explorer and Mozilla Firefox. An easy-to-use and fast Web interface allows users to browse and upload data to the repository as well as browsing the human proteome, including protein level information such as protein function and expression.

ProteomicsDB will be available free of charge. The database will be a valuable asset for researchers in the field of life sciences as well as for the pharmaceutical and biotechnology industry. Insights from analyzing the inherent datasets can be used in biomedical research and for example in developing new drugs that operate in a more targeted way without adversely influencing other cellular processes, helping to reduce side effects.

“The vast amounts of molecular data generated in biomedical research increasingly challenge the ability of scientists to see ‘the forest for the trees,” said Prof. Dr. Bernhard Kuster of TUM. “ProteomicsDB is a significant step ahead in our research aiming at a better understanding of human disease and more informed future treatments. The software helps us and others to store, integrate and analyze experimental data in real time, allowing us to study more complex biological systems at greater depth than previously possible.”

Source: SAP