Peptides present some unique challenges for the bioanalysis by LC-MS/MS of these compounds in plasma and other biological matrices.   One main challenge for LC-MS/MS bioanalytical methods for peptides is to get similar sensitivity and specificity compared to methods for small molecules.   The challenge presented by peptide for sensitivity and specificity are due to the following properties common to most peptides:

1. Peptides generally form multiple charge states which dilutes the precursor signal.
2. Relative to small molecules, peptides have more fragmentation which further dilutes the signal.
3. Endogenous peptides can cause high background.
4. Peptides can be more difficult to extract from biological matrices thus yielding lower recovery.

Despite these inherent challenges from peptides, at Pine Lake Laboratories we have developed and validated LC-MS/MS bioanalytical methods for peptides that met the required sensitivity and specificity.   We have used mixed mode solid phase extraction to help reduce background from similar peptides while still maintaining good recovery of the target peptide.  When properly tuned and with optimized chromatographic conditions, our Waters Xevo TSQ UPLC-MS/MS instruments can achieve the needed sensitivity.

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