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  • Jun 14 06:57

    lars20070 on metadata

    (compare)

  • Jun 13 17:20

    lars20070 on metadata

    whitelist only spectra_data (compare)

  • Jun 13 16:37

    lars20070 on metadata

    fix TOPP tests by whitelisting … (compare)

  • Jun 12 08:17

    lars20070 on metadata

    fix TOPP tests (compare)

  • Jun 12 07:39

    lars20070 on metadata

    rename static function (compare)

  • Jun 12 07:26

    lars20070 on metadata

    move number of samples to stati… (compare)

  • Jun 12 06:58

    lars20070 on metadata

    set correct number of MS run pa… set correct number of MS run pa… (compare)

  • Jun 11 07:16

    timosachsenberg on metadata

    Apply suggestions from code rev… (compare)

  • Jun 11 06:43

    lars20070 on metadata

    add missing meta data to FFMult… (compare)

  • Jun 11 05:30

    lars20070 on metadata

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  • Jun 06 2019 06:09

    lars20070 on mzTabTargetDecoy

    (compare)

  • Jun 06 2019 06:08

    lars20070 on develop

    [UPDATE] THIRDPARTY SIRIUS4 bui… Merge remote-tracking branch 'u… Merge pull request #4143 from o… and 1 more (compare)

  • May 10 2019 11:25

    jpfeuffer on mzTabTargetDecoy

    forgot semicolon (compare)

  • May 10 2019 11:19

    jpfeuffer on mzTabTargetDecoy

    [FIX] Lifetime of temporary lam… (compare)

  • May 09 2019 11:30

    lars20070 on mzTabTargetDecoy

    [INTERNAL] correct code style (compare)

  • May 08 2019 10:19

    lars20070 on mzTabTargetDecoy

    [TEST] fix TOPP tests (compare)

  • May 08 2019 10:07

    lars20070 on mzTabTargetDecoy

    [INTERNAL] remap column in cons… (compare)

  • May 08 2019 09:50

    lars20070 on mzTabTargetDecoy

    [INTERNAL] define addUserValueT… (compare)

  • May 08 2019 09:27

    lars20070 on mzTabTargetDecoy

    [INTERNAL] remap column in feat… (compare)

  • May 08 2019 08:36

    lars20070 on mzTabTargetDecoy

    [API] new method for remapping … (compare)

Lucas Kook
@LucasKook
@lars20070 That's what I just wrote =)
Lars Nilse
@lars20070
@MFreidank For TMT you can do the conversion ”by hand”. Read peptides.txt and use Reporter intensity i as peptide intensities. Peptides without IDs we do not need (for now).
DilzaTrevisan
@DilzaTrevisan
@MFreidank Thanks for the MQ2mzTab script, it worked with TMT files, I will now take a close look in the intensities to compare.
@MFreidank One more thing, I tried to run the report in the generated mzTab file and it crached. This is the pathway where you would find the mztab D:\data\Dilza\MQ_TMTlys_Acetyl_as_fixed\TMT_Nterm_and_Lys_Oxidation_as_variable``
Lars Nilse
@lars20070
@MFreidank As Dilza said, mzTab2report crashes on the above file on the server.
Moritz Freidank
@MFreidank
@lars20070 does this look like the error we already know about or is this something new?
@DilzaTrevisan thanks for your feedback, glad the TMT script worked. I will take a look at the mzTab2report issue.
Lars Nilse
@lars20070
@MFreidank Looks like the old Windows bug. Plots are generated alright, see DT52_etal subfolder.
You are not copying Sweave.sty into the subfolder. Please fix.
Moritz Freidank
@MFreidank
@lars20070 ProteomicsScripts/ProteomicsScripts#16
Lars Nilse
@lars20070
FYI, how to convert Skyline libraries to OpenSwath.
Lars Nilse
@lars20070
@Matthias313 @ChiayiChen Here OpenMS/OpenMS#3686 our open question regarding GluC.
Lars Nilse
@lars20070
Lars Nilse
@lars20070
MS-GF+ does not support V8-(D)E. In order to be consistent, we will use glutamyl endopeptidase for Glu-C data in all workflows.
Lars Nilse
@lars20070
@ssehztirom Let's discuss the Sirtuin analysis here. Easier for @oliverschilling to follow.
BM4120-23.png
Whitelist with charges 2+, 3+ and 4+ covers full RT range.
Lars Nilse
@lars20070
Workflow Hub with TMT and MS-GF+/Percolator workflows among others.
Lars Nilse
@lars20070
Lars Nilse
@lars20070
UK192_193_205.png
UK192_193_205_zoom.png
@ssehztirom @kernursula And here whitelisted peptides (i.e. present in all samples) for Ursula's UK181-209 urinary biomarker data. As you can see, only minimal RT alignment is necessary.
Lars Nilse
@lars20070
@ssehztirom We try to read Ursula's LFQ MQ results with MSstats, see here. But it's not so easy.
Can you please send us the R snippet which you use to read Ursula's MQ analysis? Thanks.
Lars Nilse
@lars20070
@algom @LucasKook Perhaps you have existing R code for reading MQ LFQ analyses which we can re-use? Thanks.
Lars Nilse
@lars20070
@MFreidank MQ2mzTab crashes on D:\data\Chia-Roche\CC334_341\combined\txt. TMT data.
Melanie C. Föll
@foellmelanie
Hi all, is there an easy way to obtain protein (sequence) coverage and number of peptides per inferred protein? At the moment I have to run peptide indexer after protein inference (fido+FDR+IDfilter), then mzTab exporter and to obtain the peptide numbers I have to calculate this by myself on the PSM section of mzTab export...peptide count is in my opinion important enough to export the number directly in the mzTab protein section.
@lars20070 @MFreidank @Matthias313 @oliverschilling
Lars Nilse
@lars20070
@foellmelanie Please make sure that write_protein_sequence = true in PeptideIndexer. That should result in the coverage being reported.
Lars Nilse
@lars20070
The coverage is then written to the idXML and can be exported with SequenceCoverageCalculator.
Melanie C. Föll
@foellmelanie
Thanks for pointing this out, this is completely unintuitive to me. Why would I calculate the protein coverage with a tool that is called peptide indexer and nowhere is written that write_protein_sequences also adds the sequence coverage on the other hand the added protein sequence is completely unnecessary and only increases file size and computation time...I hope the protein coverage column in mzTab and text exporter is still valid in 2.4 as I do not see the point of having an extra tool calculating only the sequence coverage? I am a bit confused...
Lars Nilse
@lars20070
Let's move the discussion to https://gitter.im/OpenMS/OpenMS. I agree with you and do not know why @cbielow needed to this SequenceCoverageCalculator tool.
Lars Nilse
@lars20070
@foellmelanie It appears in the TextExporter output. But I want to move to mzTab now.
Melanie C. Föll
@foellmelanie
I am working with 2.3 and there it appears in both TextExporter and MzTabExporter when the write_protein_sequenceswas set to true. I was just wondering if the information is still available with both exporters when there is an extra tool for the sequencecoverage in 2.4 ...
Lars Nilse
@lars20070
Please ask @cbielow in the public chat room. If it's legacy code, we will remove the tool.
oliverschilling
@oliverschilling
Pls see my post: OpenMS/OpenMS#3853
note: PeptideIndexer crashes when I set write-sequences = true
This is basic and needs to be fixed
Lars Nilse
@lars20070
@oliverschilling Can you please point me to workflow and input data? I would like to reproduce the crash. Thanks.
oliverschilling
@oliverschilling
D:\data\sgbm\2018\ID-example
Lars Nilse
@lars20070
@oliverschilling Please see my comment in https://github.com/OpenMS/OpenMS/issues/3853#issuecomment-441570724.
Lars Nilse
@lars20070
@oliverschilling For the record, I see clear, high-intensity 6+ in the Taspase data. We should search for 1+ to 7+ in the future.
Lars Nilse
@lars20070
Charge6.png
@oliverschilling BM3727 RT=2340 mz=664 z=6+
Lars Nilse
@lars20070
@oliverschilling FYI, no protein FDR before inference. See your issue #3853 above.
Lars Nilse
@lars20070
@foellmelanie Here another MALDI user. Maybe you can give him advice?
Melanie C. Föll
@foellmelanie
Unfortunately not, I never used OpenMS for MALDI data.
Lars Nilse
@lars20070
:+1:
Lars Nilse
@lars20070
If you cannot access UniProt with the UniProt.ws package Bioconductor/UniProt.ws#9 you might want to set the following option.
option(url.method="libcurl")
Lars Nilse
@lars20070
For package installations, you can circumvent https this way.