Monocle converted mzml files make FragPipe crash at the LFQ step

[Peer2011]

Dear developer of Monocle,

We tried to use Monocle for Raw file conversion before searching and quantifying our files via Fragpipe. Everything goes fine until the step of quantification when Ionquant tries to write the tables. Here, Monocle converted mzml Files make Ioquant crash with the following error message. Any idea how to solve this problem. We converted the raw files with standard settings. Is there any more detailed documentation about Monocle. Could not find many information on how to use it besides the readme file. Is there any way to run Monocle on multiple files with a more simpler command (*.raw ???). Thanks a lot for your efforts.

Best, Peer

[Peer2011]

Sorry, I forgot to attach the error message.

021-10-27 15:02:27 [INFO] - requantify = 0 2021-10-27 15:02:27 [INFO] - writeindex = 0 2021-10-27 15:02:27 [INFO] - filelist = C:\01_Data_Analysis\FRAGPIPE_TEST\filelist_ionquant.txt 2021-10-27 15:02:27 [INFO] - specdir = C:\01_Data_Analysis\FRAGPIPE_TEST 2021-10-27 15:02:27 [INFO] - C:\01_Data_Analysis\FRAGPIPE_TEST\1\MS(1)MSCON.pepXML 2021-10-27 15:02:27 [INFO] - C:\01_Data_Analysis\FRAGPIPE_TEST\2\MS(1)MON.pepXML 2021-10-27 15:02:27 [INFO] - Checking C:\01_Data_Analysis\FRAGPIPE_TEST\MS(1)MSCON.mzML... 2021-10-27 15:02:28 [INFO] - Checking C:\01_Data_Analysis\FRAGPIPE_TEST\MS(1)MON.mzML... 2021-10-27 15:02:28 [INFO] - Loading C:\01_Data_Analysis\FRAGPIPE_TEST\MS(1)MSCON.mzML... 2021-10-27 15:02:31 [INFO] - MS(1)MSCON has 5 compensation voltages: -70.0, -60.0, -50.0, -40.0, -30.0 2021-10-27 15:02:31 [INFO] - Building index... 2021-10-27 15:02:31 [INFO] - Writing index to C:\01_Data_Analysis\FRAGPIPE_TEST\MS(1)MSCON.quantindex 2021-10-27 15:02:31 [INFO] - Loading C:\01_Data_Analysis\FRAGPIPE_TEST\1\MS(1)MSCON.pepXML... 2021-10-27 15:02:34 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2021-10-27 15:02:34 [INFO] - Quantifying... 2021-10-27 15:02:34 [INFO] - Loading C:\01_Data_Analysis\FRAGPIPE_TEST\MS(1)MON.mzML... 2021-10-27 15:02:37 [INFO] - Building index... 2021-10-27 15:02:37 [INFO] - Writing index to C:\01_Data_Analysis\FRAGPIPE_TEST\MS(1)MON.quantindex 2021-10-27 15:02:37 [INFO] - Loading C:\01_Data_Analysis\FRAGPIPE_TEST\2\MS(1)MON.pepXML... 2021-10-27 15:02:39 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2021-10-27 15:02:39 [INFO] - Quantifying... 2021-10-27 15:02:39 [INFO] - Updating Philosopher's tables... java.lang.ArrayIndexOutOfBoundsException: -1 at com.univocity.parsers.common.DefaultContext.selectedHeaders(DefaultContext.java:62) at com.univocity.parsers.common.record.RecordMetaDataImpl.selectedHeaders(RecordMetaDataImpl.java:213) at com.univocity.parsers.common.record.RecordMetaDataImpl.getMetaData(RecordMetaDataImpl.java:50) at com.univocity.parsers.common.record.RecordMetaDataImpl.metadataOf(RecordMetaDataImpl.java:114) at com.univocity.parsers.common.record.RecordMetaDataImpl.getObjectValue(RecordMetaDataImpl.java:374) at com.univocity.parsers.common.record.RecordImpl.getString(RecordImpl.java:113) at o.(Unknown Source) at ionquant.IonQuant.main(Unknown Source) 2021-10-27 15:02:42 [ERROR] - -1

[Peer2011]

We compared MSConvert vs. Monocle.

[Peer2011]

We found that Ioquant cannot extract any information on the FAIMS compensation voltage from Monocle transformed mzml files. In the MSconvert generated mzml it exists.

[rrad42]

Thanks for pointing out the issue. I added FAIMS compensation voltage to the mzML output so you can download the latest version and try it out. It's possible that's not the cause of the problem and I dont know if there a way to see the source of Fragpipe at the lines shown in the error.

Re: running multiple files at once, wildcards can behave differently between operating systems but we can try to add that in the near future.

[Peer2011]

Thanks a lot for your help!!! I will try immediately and let you know.

Von meinem iPhone gesendet

Am 29.10.2021 um 07:04 schrieb rrad42 @.***>:

 Thanks for pointing out the issue. I added FAIMS compensation voltage to the mzML output so you can download the latest version and try it out. It's possible that's not the cause of the problem and I dont know if there a way to see the source of Fragpipe at the lines shown in the error.

Re: running multiple files at once, wildcards can behave differently between operating systems but we can try to add that in the near future.

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[Peer2011]

Hey guys, How to install the new version. Could you let us know how to do that. What is the difference between Monocle.CLI (Command Line Interface ???), Monocle.UI (User Interface??). How to get installed Monocle.UI. We just tried Monocle.CLI so far. Shall I just download the repository??

[rrad42]

Sorry I neglected to hit publish on the new version. There is also a prebuilt Monocle UI release now (thanks to Devin). I updated the releases and the version numbers will look a little different, but head to the releases page to see the new downloads.

The UI version actually shows a window, allows you to convert multiple files at once, and you can drag and drop them in, so you'll likely find it more convenient.

[Peer2011]

Hey guys, Quantification works with the new version :) and improves Identified peptides roughly be 5%. Now, I am interested to see how monoisotopic mass correction improves match between runs for label free quantification. To do so I need to convert a lot of raw files. Is it somehow possible to convert multiple files with one command on the cmd. I tried with Monocle.CLI - f *.raw - t mzml on the command line. However, this returns an error code. Thanks a lot for your help. Best, Peer

[mammmals]

The multi-file CLI will require a bit more work to build and test, though the UI can currently do this using the FileProcessor functionality. I opened a new issue for the functionality: #32