how to visualize maxquant results by using PDV command line ?

[BiGump123]

my command:
java -jar /share/liuqi/ganyuli/proteome/software/PDV-1.7.4/PDV-1.7.4.jar
-r combined
-rt 5
-s .
-st 1
-i tab2.txt
-k s
-o output
-a 0.5
-c 5
-pw 1
-fw 800
-fh 400
-fu px
-ft pdf
Possibly, I didn't set the corret input data format, so always appeared this error when I used the command line for visualizing maxquant results:
Exception in thread "main" java.lang.NullPointerException
at java.base/java.io.FileInputStream.(FileInputStream.java:149)
at java.base/java.io.FileReader.(FileReader.java:75)
at PDVCLI.MaxQuantImport.parseParameters(MaxQuantImport.java:1024)
at PDVCLI.MaxQuantImport.(MaxQuantImport.java:162)
at PDVCLI.PDVCLIMainClass.importFile(PDVCLIMainClass.java:669)
at PDVCLI.PDVCLIMainClass.runCMD(PDVCLIMainClass.java:389)
at PDVCLI.PDVCLIMainClass.(PDVCLIMainClass.java:229)
at PDVGUI.gui.PDVMainClass.main(PDVMainClass.java:282)

So what is the correct input data format for visualizing maxquant results by command line?

[wenbostar]

Do you want to generate figures for all spectra or just some spectra using command line?

[KaiLiCn]

Hi,

First, please copy the parameter file "mqpar.xml" into the combined folder (the reason causing this error). You could put all interested pure peptide sequences in your "tab2.txt" and set -k p. PDV will output all PSMs with the peptide sequence you input. Other parameters look good to me.

Please let me know if it still doesn't work.

Kai

[BiGump123]

Dear Kai,

Thank you very very very much! After I moved the mqpar.xml into the combined folder, than it did work! The figures sucessfully generated finally. Next, I would try to generate figures for a large scale spectra by using command line.

best wishes!

Yuli Gan

[BiGump123]

Dear wenbostar,
Sincerely Thanks for your reply! I want to generate figures for my interested peptide sequences, and Kai's opinion helped me. Next, I would try to generate figures for a large scale spectra by using command line. If there were problems, I would touch you again. In addtion, If the PDV mannual updated, containing kai's opinions for command line, that would be perfect for using PDV command line!

best wishes !

Yuli Gan

[BiGump123]

Come back for help again!

My command:
java -jar /data2/users/ganyuli/proteome/software/PDV-1.7.4/PDV-1.7.4.jar \

-r combined
-rt 5
-s .
-st 1
-i scan_number.txt
-k s
-o peptide
-a 0.5
-c 5
-pw 1
-fw 800
-fh 400
-fu px
-ft pdf

The error: Spectrum 'RawFile: P16186-11 Index: 20198 Charge: 3' in mgf file 'P16186-11.mgf' not found

The PDV will generate the mgf file, I don't know why there is no 'RawFile: P16186-11 Index: 20198 Charge: 3'. I think the PDV should generate all the Index number,is the reason that the combined folder position had been fixed or I used new maxquant version(2.4.11)?

Need your help!
Thank you!

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/data2/users/ganyuli/proteome/software/PDV-1.7.4/lib/slf4j-log4j12-1.6.1.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/data2/users/ganyuli/proteome/software/PDV-1.7.4/lib/logback-classic-1.1.6.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
P16186-11 = 17289
java.io.IOException: Spectrum 'RawFile: P16186-11 Index: 20198 Charge: 3' in mgf file 'P16186-11.mgf' not found.
at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:633)
at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:293)
at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getPrecursor(SpectrumFactory.java:261)
at PDVCLI.MaxQuantImport.parseResults(MaxQuantImport.java:736)
at PDVCLI.MaxQuantImport.addAllSpectrumFiles(MaxQuantImport.java:623)
at PDVCLI.MaxQuantImport.generateNewMGFFile(MaxQuantImport.java:579)
at PDVCLI.MaxQuantImport.(MaxQuantImport.java:174)
at PDVCLI.PDVCLIMainClass.importFile(PDVCLIMainClass.java:669)
at PDVCLI.PDVCLIMainClass.runCMD(PDVCLIMainClass.java:389)
at PDVCLI.PDVCLIMainClass.(PDVCLIMainClass.java:229)
at PDVGUI.gui.PDVMainClass.main(PDVMainClass.java:282)