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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

New Data Indicate Pressure BioSciences’ Novel Technology Platform Offers Great Promise to the Areas of Biomarker Discovery and Drug Development

Pressure BioSciences, Inc. (Nasdaq:PBIO) (“PBI” and the “Company”) announced recently that data supporting important advantages of PBI’s powerful and enabling Pressure Cycling Technology (“PCT”) Platform were presented last week at the 56th Annual Meeting of the Biophysical Society in San Diego, CA and this week at the 8th Annual US Human Proteomic Organization (“HUPO”) Conference in San Francisco, CA.

Thermo Fisher Scientific Opens New Biomarker Translational Center

Thermo Fisher Scientific Inc., the world leader in serving science, today announced at the Human Proteome Organization (HUPO) 2011 World Congress the establishment of a new Biomarker Translational Center (BT Center). The purpose of the BT Center is to accelerate mass spectrometry (MS)-based biomarker discovery research and its translation into the development of routine clinical assays for subsequent commercialization. Based in Cambridge, Mass., the BT Center combines advanced expertise from across Thermo Fisher including its B·R·A·H·M·S product line and the team at the Biomarkers Research Initiatives in Mass Spectrometry (BRIMS) Center.