How to Interpret Proteomics Mass Spectrometry Data
Proteomics mass spectrometry data are obtained using a mass spectrometer to analyze protein composition and structure. Observing and interpreting mass spectra requires understanding the basic components and features of the spectra.
Basic Features of Mass Spectra
1. X-axis
Represents m/z (mass-to-charge ratio).
2. Y-axis
Represents intensity (usually relative intensity, not directly comparable between different spectra).
Common Types of Mass Spectra
1. MS1 (Primary Mass Spectrum)
Displays the m/z and corresponding intensity of all single charged ions of a protein/peptide after ionization.
2. MS2 (Secondary Mass Spectrum)
Shows the m/z and intensity of fragment ions from a specific precursor ion (a particular peak from MS1).
Steps for Observation and Interpretation
1. Examine the MS1 Spectrum
(1) Multiple Charge Ion Series: The m/z difference between adjacent peaks corresponds to the mass-to-charge ratio of one or more protons.
(2) Isotope Distribution: A series of smaller peaks following each peak reflect isotope ions.
2. Examine the MS2 Spectrum
(1) b and y Ion Series: Fragment ions typically break at the amino acid side chains of the protein/peptide, forming b and y ions.
(2) Neutral Loss: Look for common neutral losses, such as water or ammonia molecules.
(3) Cleavage Sites: Consider possible cleavage sites on the peptide to help understand the origin of fragment ions.
Interpretation and Identification
1. Database Matching
Match fragment ion data from MS2 with predicted fragments in a database for protein/peptide identification.
2. Peptide Pairing
Pair the MS2 spectrum with candidate peptides to find the best match.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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