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Douglas McCloskey
@dmccloskey
OK sounds good. At least for tomorrow, I would be available after 14.00
Hannes Roest
@hroest
I think target-decoy on MS1 level is tricky
but we do have some experience with this as well (Oliver has data on only using MS1 data even though with some caveats)
I think you could also look at the AMT approach by Dick Smith for peptides and I think Lukas Kall has published an approach for FDR on MS1 level only
but there is not much great stuff out there as far as I am aware
but yes lets set up a meeting
Shubham Gupta
@shubham1637
I am trying to use MSChromatogram class in my application.
I am facing an error with getProduct() function, does anyone know where is it defined?
https://github.com/OpenMS/OpenMS/blob/ead8f6ff000b2d09c194edd2ce2b1360d1a8a958/src/openms/source/KERNEL/MSChromatogram.cpp#L101
andyquaile
@andyquaile

Hi all, I am trying to perform an 'AccurateMassSearch' on some MS1-only metabolomics data and since the experiment was performed in yeast, I replaced the HMDBMapping.tsv and HMDB2StructMapping.tsv with equivalent files created from data downloaded from YMDB...the structure data file available online only contains entries for the first ~2000 metabolites in YMDB so I don't have a 1:1 mapping of IDs yet and Since AccurateMassSearch requires these mappings to be equivalent the search will not run.

From what I understand however the SMILES and InChI are only used for result annotation, so I was wondering why this requirement exists? I can imagine there are plenty of other situations where it would be prohibitively difficult to retrieve SMILES/InChI IDs for a given list (i.e. any reasonably large custom database, or working in any other species other than humans). Moreover, is there a way I can work around this requirement other than perhaps creating empty/placeholder entries for the ~14000 missing IDs

M Bernt
@bernt-matthias
Are there somewhere notes / instructions how the binaries in https://github.com/OpenMS/THIRDPARTY have been built? I'm asking because I would like to add maracluster to bioconda .. and failed so far bioconda/bioconda-recipes#21472 bioconda/bioconda-recipes#19219
jpfeuffer
@jpfeuffer
Hi @andyquaile AccurateMassSearch was indeed designed with databases in mind that would have a 1:1 mapping between ID and structure. If you do not care about possible different structures, you could try to just create one entry for the molecules with the same mass and append their IDs/names to one with e.g. a comma as a separator. Maybe that would work. Other than that, there is the placeholder solution you mentioned or a change in the underlying code.
@bernt-matthias for most of the executables we have a Readme with them but it seems like there is none for maracluster.
M Bernt
@bernt-matthias
unfortunate .. if there is someone with experience then comments in the linked issues would be very welcome
andyquaile
@andyquaile
@jpfeuffer thanks for the suggestions. It sounds like the placeholder solution may be the path of least resistance for now, particularly since the 1:1 data does in fact exist somewhere in this case.
JeffEdge
@JeffEdge
Hi all! I am using pyopenMS to create a LCMS file (following heavy preprocessing) for upload by a postprocessing tool. This tool is rather picky and I need quite a few classes. I have been using the MSspectrum() class rather successfully with the exception of setLevel() which behaves unoptimally when two objects of different level are added to an exp. If the first object uses setLevel(1) than all subsequently added objects partly inherit the a level of 1. This is not the case for level >1. This can be visualized in TOPPview where the result/display is also different from a standard (instrument generated LC-MS file). BUT MY MAIN QUESTION is how to use the InstrumentSettings() constructor to create an object enabling setPolarity(), setScanMode(), setScanWindows()? Basically I want to change the corresponding parameters and save the metaData as well as the Data to a mzML file. I am exploring CachedmzML.store() but I badly in need of a working example! Thanks for the very python library!
Timo Sachsenberg
@timosachsenberg
Regarding you first question. can you post a code snipped? it sounds as if the same object might be added multiple times
JeffEdge
@JeffEdge
Hi Timo, I added a snippet to the question. Thanks!
Timo Sachsenberg
@timosachsenberg
if you have an MSSpectrum s
I think you can just do s.setInstrumentSettings(is)
with
InstrumentSettings is = InstrumentSettings()
Polarity p = IonSource.NEGATIVE (not tested)
is.setPolarity(p)
if that doesn't work we might need to check if the InstrumentSettings are properly wrapped in pyOpenMS
if not we can easily fix that
JeffEdge
@JeffEdge
Thanks: ix = InstrumentSettings()
ix.setPolarity(2)
s1.setInstrumentSettings(ix)
works!
Hannes Roest
@hroest
to be more readable and portable you could use pyopenms.IonSource.Polarity.NEGATIVE
Shekhar Shukla
@24sharkS
Hi All! I was looking for complete documentation of pyopenMS API. This link for the manual http://proteomics.ethz.ch/pyOpenMS_Manual.pdf doesn't seem to work. Can anyone suggest where to find it?
Timo Sachsenberg
@timosachsenberg
Hi! Seems the site is down. I contacted Hannes and hope he can fix that.
Hannes Roest
@hroest
The Manual.pdf is more a reference text and it seems to be hosted on a server that is gone
however https://pyopenms.readthedocs.io/en/latest/ is a good start for documentation / manual
pyOpenMS_Manual.pdf
here is a version of the pdf that I just uploaded @24sharkS
Shekhar Shukla
@24sharkS
Thanks a lot @hroest!
Arash-Omidvar
@ArashOmidvar1_twitter
hello
hello, can you help me to make a spectrophotometer? I need for my laboratory. thanks
Timo Sachsenberg
@timosachsenberg
Sorry. Only know how to build software :smile:
Arash-Omidvar
@ArashOmidvar1_twitter
software for what type spectrophotometer ?
jpfeuffer
@jpfeuffer
Mainly liquid-chromatography coupled mass-spectrometers: https://en.wikipedia.org/wiki/Mass_spectrometry
Arash-Omidvar
@ArashOmidvar1_twitter
OK do you have open source mass spectrometer ?
Timo Sachsenberg
@timosachsenberg
Only software
litian4911
@litian4911
图片.png
Hi all, Does anyone know why it went wrong? I was doing 4D DIA and there is a problem in the scoring step
litian4911
@litian4911
what's more, does anyone know how to get irt_file.tsv, which is needed in MOBI-DIK Library Generation http://openswath.org/en/latest/docs/librarygeneration.html
MahmoudGhaznavi
@MahmoudGhaznavi
Hi @litian4911 . pi0<=0 might be solved by setting parameter "--ss_main_score" to one of "VAR_XCORR_SHAPE" or "VAR_YSERIES_SCORE" in pyprophet score command. Try "VAR_XCORR_SHAPE" first.
litian4911
@litian4911
@MahmoudGhaznavi Thank you very much for answering my question, but these two methods still do not work
MahmoudGhaznavi
@MahmoudGhaznavi
@litian4911 sorry to hear that. usually for me that would solve the problem. I guess you can set some of the other parameters to different values to see if that would work. parameter "--xeval_num_iter" is for number of cross validation iteration, by default is 10, you may reduce that to 3. Also try to set new values to "--ss_initial_fdr" and "--ss_iteration_fdr".
MahmoudGhaznavi
@MahmoudGhaznavi
try 0.2 and 0.01 for those two parameters
Scott McCain
@jspmccain
Is there a way to get the instrument method using OpenMS from a .raw file or a .mzML file?
jpfeuffer
@jpfeuffer
Hi @jspmccain . Can you give an example of what you mean with "instrument method"? After loading an mzML file into an MSExperiment object, you should be able to extract information like this with the getExperimentalSettings function. E.g. in pyopenms
exp = MSExperiment()
MzMLFile().load("test.mzML", exp)
settings = exp.getExperimentalSettings()
instrument = settings.getInstrument()
print(instrument.getName(), instrument.getVendor())