disulfide crosslink analysis import

[talpa25]

Hi Mike,
sorry for bothering again. How do I manage to import results from disulfide crosslinking analysis? Here pLink generates 2 different *.plink files e.g.:
pLink_task_2020.12.09.16.56.21_disulfide_basic_ss.plink
pLink_task_2020.12.09.16.56.21_disulfide_complex_ss0.plink

The import or converting of the "basic" one with the proxl-plink converter is working,

I also tried to import the "complex" plink file data but this gives an error:

java -jar plink2toProxlXML.jar -p c:*\pLink_task_2020.12.09.16.56.21_disulfide_charge2+\pLink_task_2020.12.09.16.56.21_disulfide_charge2+_complex_ss0.plink -o "c:*\pLink_task_2020.12.09.16.56.21_disulfide_charge2+"\output_disulfide_complex.proxl.xml -f c:***\20201119_pisum_mE_OEV_XL-MS.fasta
pLink 2.x to proxl XML converter
Author: Michael Riffle [email protected]
See: https://github.com/yeastrc/proxl-import-plink2
Version: 1.4.3

Loading search parameters... Done.
Loading search results... Got error processing pLink result:
Fields: [Ljava.lang.String;@2474f125
Reason: Unexpected syntax for looplink peptide: CECKPGYAGNGIICGE(1;3;14)

Encountered an error during conversion:
Unexpected syntax for looplink peptide: CECKPGYAGNGIICGE(1;3;14)

Nevertheless, the imported data from the *basic.plink file seems to be complete.

Best,
Roman

[mriffle]

Hi Roman, could you send me the pLink_task_2020.12.09.16.56.21_disulfide_complex_ss0.plink? The .plink files are the configuration files for a plink search, curious what's going on inside that plink config file that is generating results in a syntax I haven't seen before. How did you generate this file? Also, what version of plink are you using?

[talpa25]

Hi Mike,

I generated the config file as usual by a pLink search latest version 2.3.9. The disulfide crosslink search generates this double pLink files where I'm not sure what there are meant for. I guess I have to have a look in the original publication...

Best,

Roman
pLink_task_2020.12.09.16.56.21_disulfide_charge2.zip