How I Do Detect Peptides After Trypsin Digest That Will Fly In Mass Spectrometer

Question

[Fess]

How does detect peptide fragments that will fly or ionize in mass spectrometer? I have done trypsin digest of protein sequences using python. I can't seem to understand to how determine which of these fragments will ionize in mass spectrometer. I got my sequence from NCBI database with Accession number:NP_001026855.2. What factors or features would I be looking for? Any python script or algorithm or web servers that could do job will be great.

Answer 1

[Laurent]

The paper Prediction of high-responding peptides for targeted protein assays by mass spectrometry (requires subscription) might be a good start. Table 2 lists several tools: ESP Predictor (previous ref), Peptide Sieve (ref), STEPP and Peptide detectability.

However, I think that it is very important to validation your results by checking if your peptides of interest have already been detected in real experiments. You may query the PRIDE database for your protein(s) (double checking the quality of the experiment and spectra). Also, PeptideAtlas could be worth looking at, especially their transition repository.

Hope this helps.

Answer 2

[mikmaksi]

Theoretically, you should be able to see all of the trypsin generated fragments. In practice, some fragments will ionize better than others. This depends on the sequence of the peptide and on the mass spectrometer/parameters.

Try using [?]Protein Prospector[?] to generate a theoretical peptide fingerprint (go to MS-Digest, from the main page)