Analysis for SDA crosslinking not running

[ecirri]

Dear pLink team,

I am using pLink3 to run an analysis on SDA crosslinked BSA (a test sample for future analysis) but the run does not start (even for only one sample):

I have saved SDA in the xlinkx ini as following:

name24=SDA
SDA=[K X 316.1166 316.1166 334.1279 334.1279 C(15)H(16)N(4)O(4) C(15)H(18)N(4)O(5) 0 0 0)

And these are the parameter (pretty standard)

Is there a reason why the analysis is not starting? Do we need to install specific softwares or packages?

Best Regards

[NorthblueM]

Hi,

You can troubleshoot the issue following these suggestions:

1. According to the GUI logs, it appears spectra were not successfully extracted from the RAW file at the very beginning. Please refer to issue #7 or the FAQ: Self-Troubleshooting for pLink3 Crashes or Prolonged Runtime, especially the section on failed spectra extraction.

2. Make sure you added the new cross-linker SDA via the pConfig.exe plugin interface, rather than manually editing the xlink.ini text file, to ensure correct crosslinker formatting. Refer to the tutorial: add new crosslinker.

3. Since you added amino acid X, please verify that both the Mass of amino acid X in the Amino Acids tab of pConfig has been modified and its Composition is correct. By default, the mass of X is 0.

4. If needed, update pLink3 to the latest version. Starting from pLink 3.0.17, the GUI log window outputs error messages to help locate issues.

Best,
Pengzhi