SOFTWARE_SOURCES.md

Software Sources

MSConvert (Proteowizard)

For conversion from .raw files to .mzML files, I believe you need to run the Windows build of MSConvert.exe via Wine (and possibly via mono), since it uses Windows specific DLLs from Thermo to read the .raw files.
Bryson Gibbons is exploring options for this.

http://proteowizard.sourceforge.net/download.html

Linux Wine/Docker 64-bit

Following the MS-GF+ tryptic search (step 2 in PIPELINE) you use MSConvert to run MZ_Refinery (aka mzRefiner).

For that, you can use the Linux specific build of MSConvert, since it's reading and writing mzML files http://proteowizard.sourceforge.net/download.html

Linux Native 64-bit

MSConvert source code: https://github.com/ProteoWizard/pwiz

MS-GF+

• Releases (.jar file): https://github.com/MSGFPlus/msgfplus/releases
• Source code: https://github.com/MSGFPlus/msgfplus
• Requirements: java

PPM Error Charter

• Releases: https://github.com/PNNL-Comp-Mass-Spec/PPMErrorCharter/releases/
• Source: https://github.com/PNNL-Comp-Mass-Spec/PPMErrorCharter
• Requirements: mono (https://www.mono-project.com/)

MASIC

• Releases: https://github.com/PNNL-Comp-Mass-Spec/MASIC/releases
• Source: https://github.com/PNNL-Comp-Mass-Spec/MASIC
• Requirements: mono (https://www.mono-project.com/)

Note: Although MASIC.exe is a GUI application, it also has a command line interface, as shown in step 5 in PIPELINE.txt As of May 2019, we are working on a console only version that will support .mzML files (though it is still advised to process .raw files with MASIC since more information can be extracted from them).

AScore Console

• Releases: https://github.com/PNNL-Comp-Mass-Spec/AScore/releases
• Source: https://github.com/PNNL-Comp-Mass-Spec/AScore
• Requirements: mono (https://www.mono-project.com/)

R Scripts for Downstream Processing

Available at the script folder