No Intensities data in Fraction section

[HelllenaZ]

Hello!

I had a problem with data after PeptideShaker finishing. I analyzed transcriptome data from three different crustacean species (each species is one .mgf file) using SearchGUI v4.2.17 and PeptideShaker v2.2.25. SearchGUI was launched via the console and there were no problem with it. Next, SearchGUI archive was launched in PeptideShaker (not via the console). In the end I saw that the data in the “Fractions/Intensities” section was shown only for two (120523_ZMG04 and 120523_ZMG05) of three samples. For sample 240820SK01_20200824221234 there is all data except Intensities (in the screenshots this sample - third column). All files that I used are in this link: https://drive.google.com/drive/folders/1oqZszrLZXx_PuhPGMxvbD0JUxixulj5b?usp=sharing The Intensity data for all three samples is really important for me so that I can compare all three proteomes with each other. Do you have any idea how to solve this problem?

Thank you, Lena

[hbarsnes]

Hi Lena,

The reason is that one of your mgf files does not contain the precursor intensity information.

For example, in 240820SK01_20200824221234.mgf you have PEPMASS lines like this: PEPMASS=427.8648

while in 120523_ZMG04.mgf in the PEPMASS lines look like this: PEPMASS=436.781860351563 385122.78125

The second value is the precursor intensity and without this value there is no data for PeptideShaker to show in the Intensities tab in the Fractions section.

Best regards, Harald

[HelllenaZ]

Hello Harald,

thank you for your comment! Using another program we converted original .raw files into new .mgf and now PeptideShaker's results has Intensities data =)