Targeted tyrosine phosphorylation profiling in precision oncology using SureQuant pTyr.

Tyrosine phosphorylation (pTyr) plays a pivotal role in signal transduction and is commonly dysregulated in cancer, so profiling tumour pTyr levels may reveal therapeutic insights critical to combating disease. However, the relative rarity of pTyr sites makes this approach reliant on enrichment strategies and substantially higher sensitivity than existing profiling methods provide.

High sensitivity, mass spectrometry (MS)-based pTyr methods make an attractive alternative, although the three typical data acquisition strategies – Data-dependent acquisition (DDA), targeted, and data-independent acquisition (DIA), each have limitations of their own, necessitating a trade-off between broad coverage, reproducibility, and accurate quantification.

To address this, Stopfer et al. describe a novel, high-density, targeted MS approach, termed ‘SureQuant pTyr’. It couples pTyr enrichment to accommodate low sample input (using commercially available reagents) with nano-high-performance liquid chromatography (nano-HPLC) IonOpticks Aurora Series columns, and data acquisition method templates, for a streamlined, robust, “plug and play” workflow.

Adapted from traditional Internal Standard parallel reaction monitoring (IS-PRM), ‘SureQuant pTyr’ employs internal standard trigger peptides to efficiently guide MS acquisition in real-time, expanding the capacity of targetable nodes and enabling reliable, accurate quantification of several hundred tyrosine phosphorylated peptide targets commonly dysregulated in cancers.

The authors establish the clinical applicability of ‘SureQuant pTyr’ by profiling pTyr signalling levels in human colorectal tumours, using minimal sample input, to characterise patient-specific oncogenic-driving mechanisms. In some cases, profiles aligned with previously reported molecular characterisations, but instances of new insights using pTyr characterization were also found, emphasising the complementary nature of pTyr measurements with traditional biomarkers.

The turn-key nature of this approach opens the door to rapid and reproducible pTyr profiling in research and clinical settings alike, with applications in precision medicine.

Read the full paper
High-Density, Targeted Monitoring of Tyrosine Phosphorylation Reveals Activated Signaling Networks in Human Tumors.
Cancer Res (81) (9) 2495-2509; 1 May 2021. doi: https://doi.org/10.1158/0008-5472.CAN-20-3804

Stopfer L, Flower C, Gajadhar A, Patel B, Gallien S, Lopez-Ferrer D, and White F.

Commentary by Jarrod Sandow, PhD.

About the author
Jarrod has a background in biotechnology and completed his PhD at the Institute of Medical and Veterinary Science in Adelaide. He is a co-inventor of IonOpticks’ core technology and is driven towards developing innovative solutions for the global proteomics research community that will enable scientists and clinicians to discover more from their samples to accelerate advances in biological and medical research.