Behind the Science: Protein Quantification

Sample preparation
researcher's hands holding a pipette tip just above a microplate well, ready to dispense a small sample for analysis.

This playlist of 4 videos, hosted by Waters’ Jennifer Fournier, will take you behind the science as she interviews scientists working on some of today’s laboratory toughest peptide and protein bioanalysis challenges and together they bust common myths and misconceptions.

1. “Bottoms” up: Protein quantification: bottoms up or bottom-up? As our host Jen Fournier learns, LC-MS/MS is a good alternative to ligand binding assays, and Waters scientists have been developing methods and technologies to support protein quantification for more than 8 years. Erin Chambers, principal scientist, shows Jen how to perform a surrogate peptide approach, where a protein is digested into its peptide, and a signature peptide is selected to monitor as a representative in a quantitative assay.

2. Standardization is unthinkable: You’ll be on your way up! You’ll be seeing great sights! You’ll join the high fliers who soar to high heights!” Wait – how exactly does Dr. Seuss relate to analyzing large molecules? See what our host Jen Fournier learns as she talks with Paula Orens, applications chemist and Mary Lame, principal applications chemist at Waters about a standardized protocol for protein quantification. Hint: everything gets easier with a kit-based approach when you’re talking about denaturation, reduction, alkylation, enzymatic digestion, quenching, and targeted peptide clean-up.

3. Size matters: How flexible is a kit-based approach for protein quantification? The problem is – size matters in bioanalysis, where you could be working with anything from small biomarkers to large, complicated biotherapeutics. Jen Fournier asked Paula Orens, application chemist, for a demonstration of ProteinWorks kits using a variety of different samples.

4. The Holy Grail in bioanalysis: We’re on the hunt for the holy grail: How to tackle the bioanalysis of antibody drug conjugates (ADCs). Behind the Science host Jen Fournier talks with protein quantification expert Erin Chambers about how Waters’ sample preparation kits can make ADC bioanalysis by LC-MS more tried-and-true than epically adventurous.

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