Extended install instructions

Prerequisites

MS2PIPc runs on Python 3.5 and greater. We recommend you to install a virtual environment for MS2PIPc:

python3 -m venv venv
source venv/bin/activate

Set up MS2PIPc

Download the source code of the latest release and unzip it. In the MS2PIPc project folder, you can find the required Python modules listed in requirements.txt. Install these with pip:

pip install -r requirements.txt

MS2PIPc requires some code to be compiled. For this:

  • Run the compilation with the command sh compile.sh (this can take a while…)
  • Or, alternatively, you can use the precompiled files that are posted on the release page. Extract the files in the cython_modules folder. For this option to work, Linux, Python 3.7 and Cython 0.29.2 are required!

MS2PIP is now fully set up!

Configure MS2PIPc to your use case

A few parameters need to be set in the configuration file (by default config.txt):

  • model: The peptide fragmentation method or specific MS2PIP model to employ to predict peak intensities. The available models are listed in README.md.
  • frag_error: The MS/MS error tolerance in Da. This defines the width of the region around theoretical fragment peak m/z’s where MS2PIPc looks for emperical peaks. This value is only of importance if you provide MGF spectrum files.
  • Post-translational modifications (PTMs): This part of the configuration file describes the PTMs that are present in the PEPREC file. Each line represents a certain PTM and is written as follows: ptm=name,mass-shift,opt,AA. The name should be identical to the PTM name that is used in the PEPREC file and is case-sensitive. Next is the mass-shift of the PTM in Da. The next variable is not relevant for MS2PIP, so it can be opt. Last in line is the one-letter code of the amino acid (AA) on which the PTM occurs. If a certain PTM occurs on different AAs, every AA should have it’s own line in the configuration file and have a unique name (eg PhosphoT, PhosphoS and PhosphoY). For N- and C-terminal modifications AA should be N-term or C-term, respectively. This leads, for instance, to the following syntax: ptm=name,mass-shift,opt,N-term
  • Lines can be commented out using a hashtag (#).

Prepare your input data

MS2PIP always takes a PEPREC file as input. It is a space-separated file that lists all peptides. It has the following columns:

  • spec_id: A unique ID for the peptide that, if an MGF file is given, matches with one fragmentation spectrum.
  • peptide: Peptide sequence.
  • modifications: PTMs for the given peptide. Every modification is listed as location|name, separated by a pipe (|) between the location, the name, and other PTMs. The location is an integer counted starting at 1 for the first AA. 0 is reserved for N-terminal modifications. Name has to correspond to a PTM listed in the configuration file. Unmodified peptides are marked with a hyphen (-).
  • charge: Precursor charge of the peptide.

Example of a PEPREC file:

spec_id modifications peptide charge
peptide1 - ACDE 2
peptide2 2|cam ACDEFGHI 3
peptide3 0|iTRAQ|3|Pyro_glu ACDEFGHIKMNPQ 2

In order to directly compare predictions to empirical spectra, or to create a feature-vector file to train new models, you will need to provide an MGF file. See the general README.md file for instructions on this.

Run MS2PIPc

The basic MS2PIPc syntax is as follows:

python3 ms2pipC.py PEPREC

You can also add the following optional arguments:

  -h, --help      show this help message and exit
  -c FILE         config file (by default config.txt)
  -s FILE         .mgf MS2 spectrum file (optional)
  -w FILE         write feature vectors to FILE.{pkl,h5} (optional)
  -m INT          number of cpu's to use

If you want to use another configuration file, you need to give the file location with the -c argument. The command then becomes:

python3 ms2pipC.py -c CONFIG-FILE PEPREC

That’s it! MS2PIPc should now be up and running. Instructions for more advanced use-cases (such as training your own models) can be found in the README.md file.