Re: [proteowizard-support] Error with msconvert

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Hi Samantha,

Is that Waters RAW or Thermo RAW?

If it's Waters RAW try without the peakPicking filter, because the Waters SDK can be kind of crashy with the vendor centroiding. If you need 
peak picking you can try the CWT algorithm instead of vendor. For CWT you should add an msLevel filter first so it doesn't waste time peak 
picking MS1s (because MGF format will only produce MS2s).

If it's Thermo RAW it might be a corrupt file.

In either case you can skip the files crashing for you by running a separate command for each RAW like:
FOR /D %I IN  ("L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\*.RAW") DO (C:\Program 
Files\ProteoWizard>"C:\Program Files\ProteoWizard\ProteoWizard 3.0.20258.97f41f698\msconvert.exe" %I --mgf -o "L:\NLHI Proteomics\MS 
Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\mgf" --filter "peakPicking vendor" --filter "zeroSamples removeExtra" --filter 
"threshold count 500 most-intense")

I'm not certain it will work with quotes in the FOR target. If not, cd to "L:\NLHI Proteomics\MS Projects\PRJ-0186 
VOICE\20210507-007-6006-Ec VOICE B7\raw" and then:
FOR /D %I IN  (*.RAW) DO (C:\Program Files\ProteoWizard>"C:\Program Files\ProteoWizard\ProteoWizard 3.0.20258.97f41f698\msconvert.exe" %I 
--mgf -o "L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\mgf" --filter "peakPicking vendor" --filter 
"zeroSamples removeExtra" --filter "threshold count 500 most-intense")

Hope this helps,
-Matt

On 6/1/2021 4:41 PM, Samantha Knodel wrote:
>
> Hello,
>
> I keep getting this error with msconvert generating mgfs. I have also tried with the newest version of ProteoWizard and had the same result.
>
> It generates the first but not the second.
>
> C:\Program Files\ProteoWizard>"C:\Program Files\ProteoWizard\ProteoWizard 3.0.20258.97f41f698\msconvert.exe" "L:\NLHI Proteomics\MS 
> Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\*.RAW" --mgf -o "L:\NLHI Proteomics\MS Projects\PRJ-0186 
> VOICE\20210507-007-6006-Ec VOICE B7\mgf" --filter "peakPicking vendor" --filter "zeroSamples removeExtra" --filter "threshold count 500 
> most-intense"
>
> format: MGF
>
> outputPath: L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\mgf
>
> extension: .mgf
>
> contactFilename:
>
> runIndexSet:
>
> spectrum list filters:
>
>   peakPicking vendor
>
>   zeroSamples removeExtra
>
>   threshold count 500 most-intense
>
> chromatogram list filters:
>
> filenames:
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_01_VOICE-Mix1.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_02_CAPRISA-Mix1.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_02_CAPRISA-Mix1_20210412134804.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_03_F9205BBG-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_04_E9208SLP-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_05_B9208TZK-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_06_C9205FD9-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_07_F92083G0-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_08_H9208NBB-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_09_C900G67B-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_10_F9206X9G-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_11_VOICE-Mix2.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_12_G9208TQS-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_13_H920687L-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_14_A900DK3T-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_15_J92084GK-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_16_D92094BZ-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_17_E9205G6Q-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_18_K9208B53-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_19_G9205XJ0-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_20_VOICE-Mix3.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_21_CAPRISA-Mix2.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_22_D9208PPN-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_23_F920C1VL-01.raw
>
>  L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_24_A920BF25-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_25_J920CDB1-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_26_E920C72G-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_27_D9209F7L-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_28_F9208533-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_29_F920C37Z-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_30_VOICE-Mix4.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_31_A8902J8Q-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_32_B9208GBZ-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_33_B8902CKC-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_34_J920976G-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_35_G9209L8V-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_36_E8901YGV-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_37_E9207ZW1-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_38_B92066Y0-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_39_VOICE-Mix5.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_40_G9206VK3-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_41_H920C497-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_42_DBcnt-10.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_43_B9206VDX-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_44_KAT036BR-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_45_E920892Z-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_46_F920B397-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_47_GC2061C7-01.raw
>
>   L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_48_VOICE-Mix6.raw
>
> processing file: L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_01_VOICE-Mix1.raw
>
> calculating source file checksums
>
> writing output file: L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\mgf\6006_01_VOICE-Mix1.mgf
>
> processing file: L:\NLHI Proteomics\MS Projects\PRJ-0186 VOICE\20210507-007-6006-Ec VOICE B7\raw\6006_02_CAPRISA-Mix1.raw
>
> [C:\Program Files\ProteoWizard\ProteoWizard 3.0.20258.97f41f698\msconvert.exe] Caught unknown exception.
>
> Please report this error to su...@pr....
>
> Attach the command output and this version information in your report:
>
> ProteoWizard release: 3.0.20258 (97f41f698)
>
> Build date: Sep 14 2020 21:41:26
>
> Thank you!
>
> Samantha Knodel
> Bioinformatic Analyst
>
> Burgener lab
> Center for Global Health & Diseases
> School of Medicine
> Case Western Reserve University
> 10900 Euclid Avenue
> Cleveland, Ohio.  44106
>
>
>
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