Prerequisites

• Mono
• RawFileReader from Planet Orbitrap or email jim.shofstahl@thermofisher.com with Subject “Access to RawFileReader”

Compile

Linux

mcs RawRead.cs /reference:ThermoFisher.CommonCore.RawFileReader.dll   /reference:ThermoFisher.CommonCore.Data.dll /reference:ThermoFisher.CommonCore.MassPrecisionEstimator.dll /reference:MathNet.Numerics.dll /reference:System.Numerics.dll

Windows can also use dotnet cmd “csc”

c:\Windows\Microsoft.NET\Framework\v4.0.30319\csc.exe RawRead.cs /reference:ThermoFisher.CommonCore.RawFileReader.dll   /reference:ThermoFisher.CommonCore.Data.dll /reference:ThermoFisher.CommonCore.MassPrecisionEstimator.dll /reference:MathNet.Numerics.dll /reference:System.Numerics.dll

Usage

mono RawRead.exe <ThermoOrbitrapRawfileName> <intensityThreshold>(optional) <chargeThreshold>(optional)

Windows compiled via dotnet call directly

RawRead.exe <ThermoOrbitrapRawfileName> <intensityThreshold>(optional) <chargeThreshold>(optional)

Example

• mono RawRead.exe 171010_Ip_Hela_ugi.raw (for all scans)
• mono RawRead.exe <… rawFile> 0 2 (for profile scans with charge state > 1)
• mono RawRead.exe <… rawFile> 10e6(for profile scans with recorded intensity > 1 million)
• mono RawRead.exe <… rawFile> 10e6 2 (for profile scans with charge state > 1 AND recorded intensity > 1 million)

…

Test

Search converted file with comet-ms

• normal window search for Qexactive(HF) and Canonical Human Reviewed Database

  ./comet.2018012.linux.exe 171010_Ip_Hela_ugi.raw.intensity0.charge0.MGF
  

Search Raw file directly in linux

since MaxQuant goes Linux, we can finally perform a direct search :) though there is an annoying issues of reproducibility in comparison with Windows run. It differs by ~1% which (has been reported to developers)[https://maxquant.myjetbrains.com/youtrack/issue/MaxQuant-185] and there seems to be an inherent problem in the way mono handles numbers c.f. dotnet , anyways 1% is something one can live with ;)

• Download and Install MaxQuant
• create a parameter file for all raw files in the directory using the provided generic parameter file mqparTest.xml

  for i in  *.raw; do echo $i; sed -e "s|RawTestFile|/$PWD/$i|g" mqparTest.xml > $i.mqpar.xml ; done
  

• use the paramter file(s) to search in parallel

  find . -name "*.mqpar.xml" | parallel "mono <MaxQuant_1.6.2.3 root directory>/MaxQuant/bin/MaxQuantCmd.exe  {}" 2>stdout2 1>stdout1 > stdout0 &
  tail -f stdout?
  

Compare results

awk -F '\t' '{print $1" "$6}' 171010_Ip_Hela_ugi.rawCombined/combined/txt/proteinGroups.txt | less
awk -F '\t' '{print $16}' 171010_Ip_Hela_ugi.raw.intensity0.charge0-comet-human.txt | less