MS1Connect is a tool that scores the similarity between a pair of mass spectrometry runs. This task is particularly challenging because data can be acquired under different experimental procotols. MS1Connect solves this problem by framing the problem as a maximum bipartite matching problem and by only using data fom intact peptide (MS1) scans.
We are currently developing the documentation for MS1Connect. Feel free to reach out with any questions in the meantime.
Before you run ms1connect.py you must run the makefile. You can do this by running the following command.
make
Before running MS1Connect we highly suggest you create a new enviroment (such as conda).
The inputs to MS1Connect is a set of MS1 features files. MS1Connect can generate these files for you using pyOpenMS by providing a folder of mzML files. If you prefer to use your own MS1 feature detection method you can instead provide a folder of MS1 feature files that contains the following columns: m/z, intensity, retention time, noramlized retention time (proportion of TIC), and charge.
Running MS1Connect requires running the ms1connect.py script. You can see how to run this script by running the following command.
python ms1connect.py -h
If you use MS1Connect in your work please cite:
Lin A, Deatherage Kaiser BL, Hutchison JR, Bilmes JA, Noble WS. MS1Connect: a mass spectrometry run similarity measure. Bioinformatics. 2023 Feb 3;39(2)
The manuscript describing MS1Connect can be found here.
MS1Connect requires the following:
- Python
- C++ (gcc)
- Singularity/Docker
In addition the following Python packages are required:
- pyOpenMS
- Pandas
- Numba
- Scipy
- Scikit-learn
- Matplotlib
- Seaborn