Question

You did an experiment in which you fractionated eukaryotic cells to purify the endoplasmic reticulum fraction, and you extracted the membrane proteins from this cell fraction. Next, you submit these membrane proteins for mass spectrometry analysis at the protein core facility of the university where you work. When the mass spectrometry results come back, you notice that many of the identified proteins are missing the N-terminal approximately 30 residues of the protein as it is encoded in the DNA. What is going on?

Answer 1

In secreatory proteins and type 1 membrane proteins, during the tranlsation process of mRNA , at N- terminal many amjno acids for the signal peptide. This signal peptide is recognised by Signal recognition particle.(Srp). This helps in translocation of this nascent polypeptide in translocation of this into lumen of ER. As long as it comes inside lumen, the signal peptide is cutted by signal peptidase. Thus, losing some amjno acids.

That is why the they not appear in the mature proteins