QC03 with FragPipe + RT + EICExtractor test #233
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QC03 - ALL JOBS DONE IN 3.8 MINUTES |
Peptide areaIt has been done with only EICExtractor, so without identifying first the peptide: #200 (comment) Protein and peptide countingFragPipeOpenMS |
rolivella
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Protein and peptide countingIt should be done by type of fragmentation: |
Processed file: QC03_2bf4293c4d1c8c891fab774cf973f7e9.rawFragPipeFragPipe version: 22.0 Summary
Because QC03_2bf4293c4d1c8c891fab774cf973f7e9.pepXML is empty for ETCID... |
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Could we search with PD 2.5 this QC03 HCD, etc.? Asked to Cristina. |
QC03
References: |
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As FragPipe does not work with several activation methods, we should filter as:
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If I test HCD, I get: |
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If I test ETCID: |
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OpenMS FileFilterFirst CID and HCDCID HCD Second ETCID and ETHCDI can't because: OpenMS/OpenMS#7499 |
FragPipe again for HCDAnd again the same error: |
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Opened compomics/ThermoRawFileParser#182 by suggestion of Timo S. |
Proteowizard mzML conversion + FragPipeConversionFor CID, For HCD, But I don't know for ETCID and ETHCD as refered in the doc: FragPipe |
Using PD 2.5Done by Cristina: QC03_2bf4293c4d1c8c891fab774cf973f7e9_PeptideGroups.zip Filtering only the accession from both "Accession" (Proteins file) and "Protein accessions" + "activation" (PSM file): QC03_2bf4293c4d1c8c891fab774cf973f7e9-master-high_Proteins_only_accession.csv Counting proteins: Counting peptides: |
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High-energy collision-induced dissociation - HCD |
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"Eduard" filtering strategy with FileFilter:
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Following Eduard's strategy does not work: |
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New version of FileFilter should be available in short (if not now): OpenMS/OpenMS#7499 (comment). Should be checked. |
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Why HCD filtering is not working with present FileFilter version? After doing the first selection, this is the only avtivation type left: |
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From the source code of FileFilter: https://github.com/OpenMS/OpenMS/blob/2c47a4dad7d14a1a2e3681ff94142da72fee9b64/src/openms/source/FORMAT/HANDLERS/MzMLHandler.cpp We have that for CID: else if (accession == "MS:1000133") //collision-induced dissociation
{
spec_.getPrecursors().back().getActivationMethods().insert(Precursor::CID);
}For HCD: else if (accession == "MS:1000422") //beam-type collision-induced dissociation / HCD
{
spec_.getPrecursors().back().getActivationMethods().insert(Precursor::HCD);
}For ETCID and ETHCD: else if (accession == "MS:1003182" //electron transfer and collision-induced dissociation
|| accession == "MS:1002679") // workaround: supplemental collision-induced dissociation (see https://github.com/compomics/ThermoRawFileParser/issues/182)
{
spec_.getPrecursors().back().getActivationMethods().insert(Precursor::ETciD);
}
else if (accession == "MS:1002631" //electron transfer and higher-energy collision dissociation
|| accession == "MS:1002678") // workaround: supplemental beam-type collision-induced dissociation (see https://github.com/compomics/ThermoRawFileParser/issues/182)
{
spec_.getPrecursors().back().getActivationMethods().insert(Precursor::EThcD);
} |
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I test again CID: File: Output: 3033 peptides, 797 proteins For HCD: File: Output: 2945 peptides, 774proteins But for both I got: But for instance I have: |
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Done by cchiva using PD 2.5:
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Installed last FileFilter OpenMS version:
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ETCID: ETHCD: |
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After FileFilter MS1 and FileMerger with the FileFilter output:
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Asked to Timo: OpenMS/OpenMS#7499 (comment) |
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Reply: "can you try to remove the unwanted activation? -spectra:remove_activation This seems a second version of Eduard's startegy:
I cannot do it like this because the "Select" removes all MS1 spectra and I cannot add them later with FileMerger. So I do this strategy: remove all except CID: I ran FragPipe and obtained [799,3038] For HCD: Obtained: [785,3024] For ETCID: Does not work: I checked the mzML with FileInfo and: For instance: <activation>
<cvParam cvRef="MS" accession="MS:1000598" name="electron transfer dissociation" />
<cvParam cvRef="MS" accession="MS:1003182" name="electron transfer and collision-induced dissociation" />
<cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="65.076530456542997" unitAccession="UO:0000266" unitName="electronvolt" unitCvRef="UO"/>
</activation>If I remove "electron transfer dissociation" I remove both MS:1000598 and MS:1003182 and the resulting file has no data for MS2. What can I do? Asked to Timo: OpenMS/OpenMS#7499 (comment) |
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Eduard: in the meanwhile, test Exploris data. |
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On going discussion about CV Terms for ETciD and EThcD: HUPO-PSI/psi-ms-CV#285 |
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Meanwhile, I will end the test with Q Exactive data (only CID and HCD). Steps:
Results for the file QC03_c33c611fca710ce686c0ab821692d2e7_qexactiveBut I couldn't find the isotopologues: |
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Eduard: check light isotopologues at OMSSA. Search for them and take RT apex as the reference for all isotopologues. |
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Asked Cristina for the fasta used to search QC03 on PD. |
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Ask Eduard how to configure FragPipe GUI at 100: And mass shift at UNIMOD |
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After Eduard meeting:
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I get again and again: |
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Run on Makarov for 45 min and taking punctually 40-50GB of memory. Test done at I cannot find the combined_ion.tsv with the apex RT and the ionquant is true, but at least I can find the isotopologues at peptides.tsv: |
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Ask fengchao: how to search istopoe mix with human proteome so we only search for the mass shifts for the this peptides and not all the peptides in the sample. Also, understand why we cannot see the combined_ion.tsv. |
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Asked: Nesvilab/FragPipe#1686 |
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According Fen Chao, |
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