M/Z ratios: Mass hysteria ensues

Before we run our samples on the mass spectrometer, we need to know what mass-to-charge ratios (m/z ratios) to use. By looking at the output m/z ratios of previous runs, we can assess which range to use. To do this, I examined Rhonda’s larval Crassostrea gigas mass spectrometer results.

Previous runs were generally saved on Emma’s database, which allows the user to search mass spectrometer output using a handy web interface. However, Rhonda’s data is saved on our lab computer Emu. This made the process of extracting and manipulating the files I needed convoluted. With some lab teamwork, we figured it out!

Here’s the final protocol:

• Using this R script, I randomly selected 10 of Rhonda’s samples to work with. The files I need to work with are the ones named interact..pep.xml
• I used the following code to manipulate the pep.xml file of interest. The code manipulates TPP viewer through the command line and allows me to export the data file as an .xls document.

/usr/tpp_install/tpp/cgi-bin/PepXMLViewer.cgi -C Pprobability,Gspectrum,Sexpect,Gions,Gpeptide,GMZratio,Gcalc_neutral_pep_mass,Gprotein -B exportSpreadsheet 1 -I /path/to/pep.xml/file

• I then used the following code to copy the files from Emu to my local machine

scp srlab@128.95.149.195:~/Documents/rhonda/path/to/pep.xls/file /Users/yaaminivenkataraman/Desktop

• In the R script I merged all the .xls files and created a histogram depicting the frequency of m/z ratios in the samples.

Figure 1. Frequency of m/z ratios from Rhonda’s samples

In the histogram, I can see that the majority of my peptides have m/z ratios between 450 and 950. Based on this information, Emma will set the range for my mass spectrometer runs.