De Novo Peptide Sequencing

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-De Novo Peptide Sequencing Tutorial

1st De Novo Exercise

Here is an MS/MS spectrum for you to test out your newly acquired de novo skills. Below we have an MS/MS spectrum acquired on an ion trap mass spectrometer. The first figure is the full fragment spectrum; the spectrum is then divided into three sections to make the details easier for you to see. Try not to be intimidated, just follow the simple protocol that we have described previously. Start with the high end of the spectrum, see Figure 2. We have made a pdf file for you so that you can download the spectrum and print them out so that you can get a pencil and a calculator and start sequencing. To download the spectra, right click on the link and save the pdf document to your computer.

Here are the hints:

This is a tryptic peptide ending in K or R.
The Parent [M+H]1+ mass is 1379.4
Since this is ion trap data, mass accuracy should be within 0.8u

Figure 1.

Here is a zoom in on the high end of the mass spectrum.

Figure 2.

Figure 3.

Figure 4.

Once you have done your best you can proceed onto the answer page to check out the known sequence and see some of the issues we ran into with this spectrum.

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