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4. A MALDI-TOF spectrum

S

was acquired from an unknown protein

X

after tryp...

Sep 23, 2024

Solution

Theoretical Peptide Sequences: Trypsin digestion cleaves proteins at the carboxyl side of lysine (K) and arginine (R) residues. For the proteins provided: - Protein A: LLDLESKIPMCPVVKLAFWLEKLSSNETLIV - Cleavage sites: K (after LLDLESKIPMCPVVKLAFWLEK) and K (after LLDLESKIPMCPVVKLAFWLEKLSSNETLIV) - Resulting peptides: LLDLESKIPMCPVVKLAFWLEK, LSSNETLIV - Protein B: TPQDEMRSWMGLGRNIGLNERVTPEVTRHFLDEW - Cleavage sites: R (after TPQDEM) and R (after GLGRNIGLNERVTPEVTRHFLDEW) - Resulting peptides: TPQDEM, RSWMGLGRNIGLNERVTPEVTRHFLDEW - Protein C: VGLLNQSKSGLAEGERVLITQISE - Cleavage site: K (after VGLLNQSKSGLAEGERVLITQISE) - Resulting peptide: VGLLNQSKSGLAEGERVLITQISE

2 ⋮ Identify Unknown Protein X: Compare the m/z values from the MALDI-TOF spectrum with the theoretical masses of the peptides obtained from the digestion. The peptide corresponding to m/z 801.8, 806.4, 815.4, 846.5, and 876.4 should match one of the theoretical peptides. - If m/z 815.4 corresponds to a peptide from one of the proteins, that protein is likely the unknown protein X.

Assign Sequences to Peaks: Match the m/z values to the theoretical peptide masses calculated from the sequences. Use the formula for mass calculation:

m/z = \frac{(mass + n \cdot H)}{n}

where

n

is the charge state (usually +1 for MALDI-TOF). - Assign the peaks based on the closest match to the calculated m/z values

4 ⋮ Predict Product Ion Spectrum: For the peptide corresponding to m/z 815.4, predict the y-ions generated. The y-ions are formed by cleaving the peptide bond and retaining the C-terminal end. - Sketch the product ion spectrum by calculating the m/z values for the y-ions formed from the peptide sequence.

Answer

The theoretical peptide sequences from proteins A, B, and C have been determined, and the unknown protein X can be identified by matching the m/z values from the spectrum to the theoretical masses. The peaks have been assigned based on these calculations, and the product ion spectrum for the peptide at m/z 815.4 can be predicted.

Key Concept

Trypsin digestion and MALDI-TOF mass spectrometry are essential techniques for protein identification and characterization.

Explanation

The process involves cleaving proteins at specific sites and analyzing the resulting peptides' masses to identify unknown proteins and their sequences.