Mass Spectrometry Basics
Mass spectrometry (MS) measures the mass-to-charge ratio (m/z) of molecules, providing definitive identification of your peptide's molecular composition. This technique confirms whether you received the correct peptide sequence and can detect modifications or impurities.
Key Parameters to Check
Molecular Ion Peak: The main peak should match your peptide's calculated molecular weight within acceptable tolerance (typically ±1 Da for small peptides). This confirms the correct amino acid sequence.
Isotope Pattern: Natural isotope distribution creates characteristic peak patterns. Carbon-13 and other isotopes produce smaller peaks at +1, +2 mass units that should match theoretical predictions.
Fragmentation Patterns: MS/MS analysis breaks peptides into fragments, creating fingerprint-like spectra that definitively confirm sequence identity.
Common Analysis Methods
MALDI-TOF: Matrix-Assisted Laser Desorption/Ionization Time-of-Flight is excellent for intact peptide mass determination. Results typically show [M+H]+ peaks for protonated molecules.
ESI-MS: Electrospray Ionization produces multiple charge states, creating peaks at different m/z values. Calculate the actual molecular weight from these multiple peaks.
Interpreting Results
Mass Accuracy: High-resolution instruments provide mass accuracy within 5 ppm (parts per million). Lower resolution instruments may show ±1-2 Da tolerance.
Signal Intensity: Strong molecular ion peaks indicate good peptide stability and analysis conditions. Weak signals may suggest degradation or ionization problems.
Red Flags
Be wary of results showing significant mass deviations, missing molecular ion peaks, unexpected fragmentation patterns, or mass spectra that don't match the claimed peptide sequence.
Disclaimer: This information is for research purposes only and not medical advice. Mass spectrometry analysis requires specialized equipment and expertise for proper interpretation.