This approach can further provide absolute quantitation of targeted proteins by incorporation of stable isotope-labeled peptides as internal standards (AQUA)

Make a seamless transition from biomarker discovery to targeted protein quantitation using the most selective, sensitive and automated workflow with the TSQ Vantage triple quadrupole MS and SRM Workflow Software.

Look for biomarker candidate proteins in complex matrices using an H-SRM assay on the TSQ Vantage or TSQ Quantum Ultra. High resolution Selected Reaction Monitoring (H-SRM) reduces matrix effects without loss of signal, providing more accurate quantitation and more robust assays. Discovery-based experiments provide a wealth of knowledge and thousands of MS and MS/MS spectra that can be used to direct more selective SRM-based analyses using automated SRM Workflow Software.

A common endpoint for a biomarker discovery experiment is a list of putative marker proteins. A reasonable next step is to perform targeted quantitative measurements of these proteins by monitoring proteotypic peptides in an expanded patient population to assess their validity as potential clinical markers.

Unlike in the discovery phase, hundreds of samples need to be run for the verification of the putative marker proteins. One approach for this application is the use of triple quadrupole mass spectrometry to monitor a unique peptide (or many peptides) from a protein of interest by a selected reaction monitoring (SRM) assay.

A high throughput, robust, selective and sensitive method is required for this verification stage, and the selected reaction monitoring (SRM) method with triple quadrupole mass spectrometry is ideal for this application. Although this approach gives very specific and sensitive responses for targeted peptides, it is often still difficult to differentiate between the targeted peptide signal and chemical background, particularly when detecting very low abundance proteins in highly complex samples. The unique high resolution SRM (H-SRM) capability of the TSQ Vantage and TSQ Quantum Ultra overcomes this challenge by increasing SRM assay specificity.

An H-SRM based specific, sensitive, robust assay for targeted proteins offers significant benefits for biomarker verification studies:

• H-SRM dramatically reduces non-specific interferences from complex backgrounds, improving assay specificity.
• Fast SRM cycle time: only a few milliseconds are required for each peptide transition. Because of this rapid scan time, hundreds of transitions can be easily monitored during a single LC/MS separation, with no need to "schedule" SRM experiments.
• SRM-triggered MS/MS: Using Data Dependent MS/MS, when a targeted peptide transition is detected, a full scan MS/MS spectrum can be acquired. Peptide structure can then be confirmed by MS/MS.

SRM Workflow Software:
o Predicts proteotypic peptides.
o Determines the best SRM transitions and builds the TSQ instrument method.
o Quantitates each targeted peptide.
o Utilizes MS/MS library information derived from data dependent discovery experiments acquired on Thermo Scientific LTQ ion trap-based platforms to optimize the targeted method.

This approach can further provide absolute quantitation of targeted proteins by incorporation of stable isotope-labeled peptides as internal standards (AQUA)

You can now also order additional proteomics resources, or learn about other mass spectrometry or proteomics solutions.