Investigating leukaemias using proteomics technologies from Applied Biosystems

Researchers at the University of Manchester are using an Applied Biosystems QSTAR® XL Hybrid LC/MS/MS System and a 4000 Q TRAP® LC/MS/MS System with iTRAQ™ reagents to systematically analyse the proteomes of normal and malignant stem cells, such as those involved in cancers like chronic myeloid leukaemia.

"Proteomic analysis provides us with extra information that transcriptomic analysis cannot achieve, such as post-translational regulatory mechanisms that can affect the amount and function of proteins within the cell," explained Professor Tony Whetton, Professor of Cancer Cell Biology at the University. "One of the exciting things about the iTRAQ labelling reagents is that even with tiny amounts of protein, as little as 40 mg, we can get relative quantification of 800-900 proteins from stem cells."

"Also, phosphorylation and other protein post-translational modifications can occur, which are functionally pivotal to the action of important leukaemia causing genes, including BCR/ABL and NPM/ALK. With our approach we can identify and characterise these phosphorylation sites on key specific proteins, via MS-based phosphopeptide analyses.

The QSTAR System's sensitivity and resolution are critical for relative quantification mass spectrometry, and being able to do MRM on the Q TRAP System is essential for us to perform phosphopeptide analyses with high sensitivity."

With Professor Caroline Dive, Professor Whetton is additionally acquiring an Applied Biosystems 4800 MALDI TOF/TOF™ Analyzer and another 4000 Q TRAP System for the definition of biomarkers in serum or plasma samples relating to prognosis, diagnosis and efficacy in cancer treatment.

"The complexity of serum samples demands the highest level of separation and analytical technology to find such biomarkers," said Professor Whetton. "Using these instruments provides us with great opportunities for discovering and quantifying peptides and proteins imbued with diagnostic information."