N terminal peptide modification

[adithirv]

Hi,

I am running a closed search using a set of mgf files. I am interesting in adding a peptide N terminal pyro-glu modifcation to my analysis. But MSFragger freezes after starting the process. There are no error messages given. Could you please guide me as to what may be the problem? Here is how I define the modification: 'variable_mod_04 = -17.02650 nQ'. Alternatively, I also tested another N terminal peptide modification facing the same problem: 'variable_mod_05 = -17.0106 nE'.

Thanks in advance, AR

[chhh]

@adithirv
Could you please post here the following:

• The output that gets printed in the text console (either in GUI or command line console)
• The fragger parameters file that you use. If you're using the GUI version, this file is written to the output directory that you specify.

[adithirv]

@chhh Here is the output from the console which stays the same even upto 24 hours (the max time I waited to check for progress before I kill the job).

Will execute 1 commands:
java -jar /home/bioinf/bioinf_data/33_omul/projects/bartonella_henselae/proteogenomics/msfragger_refseq_all/MSFragger/MSFragger_20170103/MSFragger.jar /home/bioinf/bioinf_data/33_omul/projects/bartonella_henselae/proteogenomics/msfragger_refseq_all/msfragger_param1_GUI_mzML/fragger.params /home/bioinf/bioinf_data/33_omul/projects/bartonella_henselae/proteogenomics/msfragger_refseq_all/msfragger_param1_GUI_mzML/cyt1_ogepep.mzML 

~~~~~~~~~~~~~~~~~~~~~~

Executing command:
$> java -jar /home/bioinf/bioinf_data/33_omul/projects/bartonella_henselae/proteogenomics/msfragger_refseq_all/MSFragger/MSFragger_20170103/MSFragger.jar /home/bioinf/bioinf_data/33_omul/projects/bartonella_henselae/proteogenomics/msfragger_refseq_all/msfragger_param1_GUI_mzML/fragger.params /home/bioinf/bioinf_data/33_omul/projects/bartonella_henselae/proteogenomics/msfragger_refseq_all/msfragger_param1_GUI_mzML/cyt1_ogepep.mzML 
Process started

fragger.params.txt

Thanks, AR

[chhh]

@adithirv There certainly is no need to wait 24h, something is wrong. Could you please provide some info about your environment?

• version of GUI you're using
• OS and version
• is it a 32 or 64 bit system
• the output of java -version or better the output in the GUI console, when you click Check Java Version button on the Run tab.
• which version fragger version do you have (just the name of the zip file you downloaded) I have just downloaded the GUI, MSFragger and Philosopher to make sure that nothing got broken, it all ran fine (Win7, Oracle Java 8).

[adithirv]

@chhh Here are the details corresponding to your questions, I am using:

• MSFRAGGER GUI v3.0
• Debian 8.4 (jessie codename)
• 64bit
• 1.8.0_121
• MSFragger build 20170103.0

Hope the information helps to resolve what they problem might be. Let me know if you need further information.

Thanks

[chhh]

@adithirv I don't see a reason for it not to work. We haven't tried it on Debian specifically, but should not matter as long as the java command is working.

• What happens if you go to the Run tab and click Check Java Version? Does it print anything?
• What happens if you try the following command from the terminal java -jar MSFragger.jar fragger.params some-file.mzML?

[adithirv]

@chhh

• This is what is printed when I click 'Check Java Version' in the 'Run' tab: Java Info: java.version: 1.8.0_121 java.vm.specification.version: 1.8 java.vm.specification.vendor: Oracle Corporation java.vm.specification.name: Java Virtual Machine Specification java.vm.version: 25.121-b13 java.vm.vendor: Oracle Corporation java.vm.name: Java HotSpot(TM) 64-Bit Server VM java.specification.version: 1.8 java.specification.vendor: Oracle Corporation java.specification.name: Java Platform API Specification
• It runs fine only if the output format is pepXML.

So, I now figured it out that the run goes into sleep when the output format from MSFragger is set to 'tsv' both on the GUI and on the command line. Hope that gives you more insight on what might go wrong here.

[andytyk]

The downstream analysis (TPP and Philosopher) is only compatible with the pepXML output. TSV output is more for getting a quick look at your data or for developers who want to couple MSFragger output to their tools but don't want to deal with the pepXML format. Let us know if you have any further issues.