error in import MS/MS

[Tanu Soni]

Hi ,

I converted .d file to mzXML using https://wiki.mpi-cbg.de/lipidx/File:MSConvertSettings.png.

I am getting an error when i try to import it.



LipidXplorer version: 1.2.6
Python version: 2.7.3 (default, Apr 10 2012, 23:24:47) [MSC v.1500 64 bit (AMD64)](2.7.3)AMD64

Importing: Pooled PLasma_MS2_QC_Neg_04.mzXML
  File "C:\software zip\LipidXplorer-1.2.6\lx\gui\lpdxGUI.py", line 485, in run
    self.resultQ.put((requestID, callable(*args, **kwds)))
  File "C:\software zip\LipidXplorer-1.2.6\lx\spectraImport.py", line 455, in doImport
    MSMSthresholdType = scan.options['MSMSthresholdType'])
  File "C:\software zip\LipidXplorer-1.2.6\lx\readSpectra.py", line 784, in add_mzXMLSample
    smpl = list(PrecursorSort(MzXMLFileReader(sample)))
  File "C:\software zip\LipidXplorer-1.2.6\lx\fileReader\mzxml.py", line 335, in next
    spectra = list(self.input)
  File "C:\software zip\LipidXplorer-1.2.6\lx\fileReader\mzxml.py", line 166, in next
    yield self.extract_scan(ele)
  File "C:\software zip\LipidXplorer-1.2.6\lx\fileReader\mzxml.py", line 115, in extract_scan
    peaks = array('f',b64decode(peakselt.text))
ValueError string length not a multiple of item size

[Rajesh Pujari]

Dear friends anf groupd members,

I have the same problem of importing spectra with the .d file from agilent that ealrier users have faced.

In case anyone sorted out this issue of import the spectra information properly, could you please help me out in this concern.

Although, to the best of my knowledge I have read all related papers and post and doing it correctly still missing some connecting link.

Please help 

[Dominik Schwudke, RC Borstel]

Hallo,

have you tried it with mzml format with MSconvert?
that might work better.

If you share a example file with me, I can have look into it.

best
Dominik

[Rajesh Pujari]

Dear Dominik,

Thanks for your support and concern, I have read google groups post from your end.

I really appreciate your support for everyone using lipidxplorer.

Meanwhile I was in touch with Dr. Ronny and he has helped me a lot in getting out of many of my issue with lipid xplorer.

I will write to you for further troubleshooting of the software.

Thanks and regards

Rajesh

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[Dominik Schwudke, RC Borstel]

Very good.
Ronny knows best.

regards
Dominik

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[Andie]

Dear Rajesh,

I am having the same problem you were facing 5 years ago, would you be able to post the solution?

This would be much appreciated.

Regards,

Andie

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[Nicholas N]

Andie,

Good question. It took me a few tries to get it to work well. I hope this is helpful.  

The command below with msconvert will get you a .mzml to import to lipidXplorer.  From there, you can follow the tutorials online for importing from .mzml to lipidXplorers .sc masterscan file.  And from there running .mfql queries to get the results you need. 

Here is an example line I use to use the command line msconvert program: 

msconvert .\*.d  --outfile "scan02m.mzml"  --32  -v --filter "peakPicking cwt snr=0.1 peakSpace=0.1 msLevel=1-" --filter "scanTime [0120,0179.99]" --filter "titleMaker <RunId>.<ScanNumber>.<ScanNumber>.<ChargeState>" 

In this case, I make a batch file that can convert any .d file
".\*.d" means look in the current directory ( where you called the batch file from) 
-- outfile says what should the name of the file be.  In this case "scan02m.mzml " stands for I want just the second minute of the run in my file 
--32 means to use 32bit floating point numbers.  This is over 7 decimal digits of precision.  https://en.wikipedia.org/wiki/Single-precision_floating-point_format   
-v is verbose so it gives you more feedback as it runs.  Once everything is running well, I'll usually ignore it. Very helpful at first, and costs nothing. 
-- filter "peakPicking cwt snr=0.1 msLevel=1-"  means that it will pick peaks using the cwt method as described in "Wavelet-Based Peak Detection and a New Charge Inference Procedure for MS/MS Implemented in ProteoWizard’s msConvert" by French .. Tabb. 2014
( I had to look it up again to be sure. Also CWT stands for Can't WaiT.  For some reason the agilent plug in for msconvert was wicked slow. The CWT made it better)   SNR = 0.1 means signal to noise ratio that I'm picking up a fair amount of noise, but also very unlikely to miss any valid peaks.  You can adjust as your preference and needs) 
--filter "scanTime [0120,0179.99]" takes only the second minute.  Adjust for the portion of the run you want, or even split into multiple files. 
--filter "titleMaker <RunId>.<ScanNumber>.<ScanNumber>.<ChargeState>"  adds a title to the start of each scan.  I've found from trial and error and  looking online that without it, especially the charge state, that lipidXplorer will not recognize the scans.  Relatedly, it's best to separate negative scans from positive scans for LipidXplorer. 

As Dominik mentioned, .mzxml is deprecated and not used much in the MS community these days.  The command above will give you .mzml.  

If you don't already have it, Andie, msconvert is part of proteowizard. Download here:  http://proteowizard.sourceforge.net/download.html 

Best wishes,

Nick

 

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[Andie]

Thanks a lot Nicholas,

As I was getting ready to follow the advise, I realised that all I had to do is to wait like 13 minutes and it all worked fine.

Not sure why it takes so long with my files but well, thought to share that sometimes we need to wait a bit longer.

Still is good to know there are alternatives :0).

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