OpenMS/OpenMS

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Hannes Roest

@hroest

yes, that is correct

so if you have different label groups, they should be recorded as different peptides

Moritz Stüve

@mostueve_gitlab

Hi, I have a bunch of M/Z values and was wondering if I can use OpenMS for their analysis? Also, since I did not find anything concerning it: can I use a filetype like .xlsx or .csv with your software? Any help is appreciated :-)

Timo Sachsenberg

@timosachsenberg

hi Moritz. What kind of data do you have and what kind of analysis do you have in mind?

Moritz Stüve

@mostueve_gitlab

Hi Timo, I have measurements from medium supernatants, which have already been transformed into masses (I think). So they are float values ranging from 150 to 1300 (or something like that). What I am looking for is the compounds these could possibly be.

Hannes Roest

@hroest

@mostueve_gitlab it really depends on what kind of experiment you did, OpenMS is desgined for quantitative analysis of proteomics or metabolomics data acquired with LC-MS/MS

Moritz Stüve

@mostueve_gitlab

Hi, the values I have are from LC-MS , exometabolomics, they are m/z values. If OpenMS is only designed to handle raw data, I might be wrong here :D

Hannes Roest

@hroest

I assume you are interested in metabolomics. What is exometabolomics? it sounds like your values are already preprocessed through another pipeline. We do have pipelines that use LC-MS data and try to identify compounds. I assume you are trying to do this based on m/z values alone, you do not have any MS2 spectra? In that case probably the best tool is AccurateMassSearch which allows you to search against a database, for example HMDB: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/a16030.html

I think @oliveralka could provide you with more pointers if you can describe better what it is you want to do (I have some trouble to understand exactly what kind of analysis you want to perform)

Moritz Stüve

@mostueve_gitlab

Hi Hannes, yes, this is what I want to to. I want to identify compounds based on the m/z values and have no further data. I will look into AccurateMassSearch, it sounds like what I need. Thanks a lot!

Oliver Alka

@oliveralka

@mostueve_gitlab Unfortunately, at least as far as I am aware, there is no easy way to just use a .tsv or .csv with m/z values, but there is a workaround. You could create a “.etda” file (https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/experimental/feature/msstats/html/classOpenMS_1_1EDTAFile.html). It is a tab separated file with “rt mz int”. Then you can use the IDFileConverter to convert the “.etda” to an openms internal “.featureXML”. The “.featureXML” is used as one of the inputs for AccurateMassSearch.

In addition you need two library files and adduct files - for this please see our Tutorial (https://www.openms.de/tutorials/) .

Hannes Roest

@hroest

@jpfeuffer @timosachsenberg this is actually a problem: https://github.com/OpenMS/OpenMS/pull/4182/files#r328248843

we cannot really deal with gcc 4.9

for example we cannot build Python wheels for manylinux with that

Timo Sachsenberg

@timosachsenberg

We discussed this and Julianus will try to revert that. In the future we might need to find a different solution e.g. using conda

Hannes Roest

@hroest

either conda or manylinux2010:

Timo Sachsenberg

@timosachsenberg

isn't manylinux2010 still gcc 4.8.2?

Timo Sachsenberg

@timosachsenberg

for conda, we probably need to create a pyOpenMS recipe similar to: https://github.com/bioconda/bioconda-recipes/tree/6c6af5b31d1deca7483ed17b4efaa1843b59b1fc/recipes/openms

Hannes Roest

@hroest

no manylinux2010 is newer

lee-s-parsons

@lee-s-parsons

When I run CometAdapter via OpenMS in KNIME, I have output that has both a "unique" and a "opt_global_protein_references" column. The latter has values of "non-unique" and "unique" while the column "unique" is boolean. Can someone help me understand the difference between the two? In the data set I am looking at right now the set of peptides marked "unique" in "opt_global_protein_references" is a very small subset of the set that was "true" for "unique".

R Greg Stacey

@GregStacey

I'm trying to generate a spectral library with PASEF data. http://openswath.org/en/latest/docs/librarygeneration.html Do I need an ion retention file for this? This would be the --irt flag in python create_library.py --irt irt_file.tsv

klannieha

@klannieha

@GregStacey that is correct, if you have pasef data then ion mobility information for the iRT would be needed, and the script performs a linear alignment.

R Greg Stacey

@GregStacey

@klannieha Naive question - how does one go about generating an irt file?

klannieha

@klannieha

@GregStacey so one way to generate it is to just run the iRT kits on pasef mode and use the MaxQuant output, or you can use multiple dda runs on pasef mode and find the high precision iRTs just like in Bruderer et al Proteomics. 2016 Aug;16(15-16):2246-56. doi: 10.1002/pmic.201500488. Epub 2016 Jun 28.

Hannes Roest

@hroest

@klannieha can you provide an example of what the irt_file.tsv looks like?

klannieha

@klannieha

Screen Shot 2019-10-15 at 10.12.58 AM.png

Hannes Roest

@hroest

@cbielow @timosachsenberg @jpfeuffer any thoughts on this OpenMS/OpenMS#4299 ?

Timo Sachsenberg

@timosachsenberg

I think you summarized that nicely. We probably need to conditionally remove the noexcept/test on windows

Timo Sachsenberg

@timosachsenberg

or implement the the move constructors

Hannes Roest

@hroest

or implement the the move constructors

well yes, that is what we did. However that is not safe, basically we are just telling the compiler: "Dont worry, OpenMS::Map is safe to move-construct and it wont throw an exception" however we are using the MSVC std::map which is not exception safe -- so what happens if std::map throws?

Timo Sachsenberg

@timosachsenberg

If it’s because of out of memory then we are lost anyways. Usually no way to recover

Timo Sachsenberg

@timosachsenberg

What about the boost versions of the stl containers?

https://www.boost.org/doc/libs/1_67_0/doc/html/container.html

I did not try it but it sounds like it might be a possible candidate for (platform specific?) replacement

Brett Phinney

@UCDProteomics_twitter

hello all openMS people :)

I have a openSWATH question if anyone can help with that

Timo Sachsenberg

@timosachsenberg

Happy to help if I can. Otherwise will try to poke some of our OpenSWATH guys ;)

Brett Phinney

@UCDProteomics_twitter

Thanks! I stared generating some diaPasef data and I just need to figure out how to reproduce that analysis

I believe all the software is included in openms 2.4

is there a good guide somewhere ?

Timo Sachsenberg

@timosachsenberg

I only know about http://openswath.org/en/latest/docs/mobi-dik.html

I guess @hroest can give you additional details

Brett Phinney

@UCDProteomics_twitter

Yes , that’s what I’d like to try . Not sure if there is an easy way to start

Hannes Roest

@hroest

yes the Mobi-DIK pipeline is our current up to date pipeline for data analysis

Brett Phinney

@UCDProteomics_twitter

Thanks Hannes, any tips on getting started with Mobi-DIK?

Hannes Roest

@hroest

depends on what you want to do - best place to start is the official website http://openswath.org/en/latest/docs/mobi-dik.html

we describe how to (i) generate the library and (ii) convert your tdf files to mzml files

with the library and the mzml file you can then run OpenSwath

Ankita Singh

@anksi0007_twitter

I am a new openMS user and would like to work with RNPxl tool.

In the openMS TOPPAS tutorial, description of RNPxl tools is provided in the utils section but for some reason, I can not find it in the util section of the TOPPAS (version 2.4.0 (9690d06)).
FYI, I have tried opening TOPPAS on both MacOS and Windows.

Can you please help me with the same?

Also, please feel free to ask if in case you need any other info from my side.

Timo Sachsenberg

@timosachsenberg

Hi Ankita. In 2.4 there should be RNPxlSearch which is slightly optimized compared to the initial RNPxl version.

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