Filtering ITMS/FTMS from Lumos data files losing all scan data

[proteowizard]

Filtering ITMS/FTMS from Lumos data files losing all scan data

[chambm]

What are your <instrumentConfiguration> sections in the resulting mzML?

[chrashwood]

Thanks for the quick reply. Comparing the filtered vs non-filtered mzml conversion: run id spectrumList is missing run id chromatogramList is the same. index name="spectrum" is different (no details present for this section and no offset values) index name="chromatogram" is different (TIC intensity is 0.001% of the non-filtered mzML file) indexedmzML, mzML, cvList, fileDescription, referenceableParamGroupList, softwareList, instrumentConfigurationList and dataProcessingList are the same.

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On Mon, Jul 30, 2018 at 1:14 PM, Matt Chambers ***@***.***> wrote: What are your sections in the resulting mzML? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#144 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Aca4SK1RGjbFD68LhdCphmdK5pKXBK1sks5uL0z5gaJpZM4VkqW0> .

[chambm]

I mean what are the contents in the <instrumentConfigurationList>

[chrashwood]

Sorry for the misinterpretation: <instrumentConfiguration id="IC1"> <referenceableParamGroupRef ref="CommonInstrumentParams"/> <componentList count="4"> <source order="1"> <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/> <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/> </source> <analyzer order="2"> <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/> </analyzer> <analyzer order="3"> <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/> </analyzer> <detector order="4"> <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/> </detector> </componentList> <softwareRef ref="Xcalibur"/> </instrumentConfiguration> <instrumentConfiguration id="IC2"> <referenceableParamGroupRef ref="CommonInstrumentParams"/> <componentList count="4"> <source order="1"> <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/> <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/> </source> <analyzer order="2"> <cvParam cvRef="MS" accession="MS:1000081" name="quadrupole" value=""/> </analyzer> <analyzer order="3"> <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/> </analyzer> <detector order="4"> <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/> </detector> </componentList> <softwareRef ref="Xcalibur"/> </instrumentConfiguration> </instrumentConfigurationList>

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On Tue, Jul 31, 2018 at 12:33 PM, Matt Chambers ***@***.***> wrote: I mean what are the contents in the <instrumentConfigurationList> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#144 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Aca4SJ8eQeaUbhFaTIWppfNXS3-m5QS6ks5uMJTbgaJpZM4VkqW0> .

[chambm]

Hmm, are you sure that your data contains FT scans? The scan filters say FTMS? Can you send a RAW file?

[chrashwood]

100% sure. It's a triggered neutral loss experiment. I've compressed the raw file so it's a 400MB zip archive. Do you have a preferred method to share the data? It's not a sensitive method/sample so can be public.

[chambm]

This will work for non-sensitive data: https://skyline.ms/filecontent/home/support/file%20sharing/begin.view?

[chrashwood]

Thanks. It's uploaded and available now.

[chambm]

I can reproduce the problem and have figured out the cause, I just haven't gotten to fix it yet. (the filter only checks the first analyzer, when it really should check the last, or all)

[chrashwood]

That's great to hear, thanks Matt! Is this problem specific for msconvert or are fixes required for the entire Proteowizard suite (I'm particularly interested in msaccess)

[chambm]

Should be fixed in #204. This problem would happen anywhere --filter is used.

[jspaezp]

Sorry for resurrecting this issue but I am having the same problem using the msconvert in ProteoWizard 3.0.18215.f6864290f

I am using this file from PRIDE
Pride repo: PXD004732
Test File: 01625b_GB2-TUM_first_pool_10_01_01-2xIT_2xHCD-1h-R1.raw

MSCONVERT="/c/Program Files/ProteoWizard/ProteoWizard 3.0.18215.f6864290f/msconvert.exe"
TESTFILE="01625b_GB2-TUM_first_pool_10_01_01-2xIT_2xHCD-1h-R1.raw"
count_filters() {
    grep -P "filter" ./out/*.mzML | grep -oP "value=\".*?ms(\d|\s)" | sort | uniq -c 
}

"${MSCONVERT}" ${TESTFILE} --filter "peakPicking true 1-" -o out/
count_filters
#   28830 value="FTMS + c NSI d Full ms2
#    3227 value="FTMS + p NSI Full ms
#   28830 value="ITMS + c NSI r d Full ms2

"${MSCONVERT}" ${TESTFILE} --filter "analyzer orbi" --filter "peakPicking true 1-" -o out/
count_filters
# EMPTY

"${MSCONVERT}" ${TESTFILE} --filter  "peakPicking true 1-" --filter "analyzer orbi" -o out/
count_filters
# EMPTY

"${MSCONVERT}" ${TESTFILE} --filter "analyzer orbi" -o out/
count_filters
# EMPTY

"${MSCONVERT}" ${TESTFILE} --filter "analyzer FT" -o out/
count_filters
# EMPTY

"${MSCONVERT}" ${TESTFILE} --filter "analyzer FTMS" -o out/
count_filters
# EMPTY

Is there anything I am doing wrong?

Kindest wishes,
Sebastian

[chambm]

Try a newer version of pwiz. Even though this issue was fixed in 2018, it seems your version manages to predate it.

[jspaezp]

Noticed the error was due to the path not using msconvert from the actual updated installation (so I guess the issue is that updating pwiz does not remove older versions, which in itself could be a design choice...)

Thanks for the reply.