include charge state array

[grandrea]

Hello,

I am trying to parse orbitrap data at the MS1 level to plot charge state distributions. Is there a way to read out charge states from the .raw file and write them to mzML using the default charge state array? I am referring to all peaks, not only precursors.

thank you

[caetera]

Hi @grandrea that will be scheduled for the next release

[grandrea]

thank you!

[caetera]

Implemented in 6ee904c

[grandrea]

thanks- d you have some steps so that I can compile from source (I see it is not as simple as dotnet restore) or should I just wait for a release?

[caetera]

Particular details depend on your platform, but in general you should be able to compile it the following steps.

1. Clone the dotnetcore branch of ThermoRawFileParser repository, for example, git clone https://github.com/compomics/ThermoRawFileParser.git --branch dotnetcore --depth 1 (depth is optional, it just saves you time/space, cloning only the last commit, instead of complete repo).
2. Make sure, you have .NET 8 SDK and runtime (you will need both) installed. Please, see https://dotnet.microsoft.com/en-us/download/dotnet/8.0 for platform-dependent instructions.
3. Download Rawfile reading assemblies as NuGet packages from Thermo's Github. You need only Net8 version - https://github.com/thermofisherlsms/RawFileReader/tree/main/Libs/NetCore/Net8 and save them somewhere locally. Unfortunately, we are not allowed to include the packages as part of this repository.
4. Include the local folder with these packages as one of the sources in Nuget, for example, dotnet nuget add source -n Thermo {path_to_local_source}. You can check configured sources using dotnet nuget list source - you should see nuget.org and your local path in the list.
5. After that running dotnet build . inside of the cloned repo (last dot means check current folder for projects, otherwise you can also provide the path to an .sln or .csproj file) you should be good. The binary will be in bin/x64/Debug.

I hope it helps.