Please download the software from


Linux or Windows

Please unzip the downloaded .zip file, and PepPre can be used directly without installation.


For macOS users, we provide both .pkg and .zip files.

We would recommend to use the .pkg file which can be installed by simply double clicking it. The software would be installed at /Applications/MesMS/ by default.

The .zip file contains the .app package software and can be used directly without installation. If the macOS says:

“” is damaged and can’t be opened. You should move it to the Trash.

Please run

sudo xattr -r -d [path/to/]

in terminal to remove the quarantine attributions.


The software provides a graphic user interface (GUI) and a command line interface (CLI). You can run the GUI by double clicking the icon of the software. For Linux and Windows users, you can find the executable files in content folder under the unzipped folder.

You can run the executable files with --help to see the usage of the CLI:

usage: PepPre [-o output] [--ipv IPV] [--mode mono|max] [-w Th]
              [-z min:max] [-e ppm] [-t (≥0.0)] [-n fold] [--inst]
              [-f csv,tsv,ms2,mgf] [-h] data...

positional arguments:
  data                  list of .mes or .ms1/2 files; .ms2/1 files
                        should be in the same directory for .ms1/2

optional arguments:
  -o, --out output      output directory (default: "./out/")
  --ipv IPV             Isotope Pattern Vector file (default:
  --mode mono|max       by mono or max mode (default: "mono")
  -w, --width Th        isolation width (default: "auto")
  -z, --charge min:max  charge states (default: "2:6")
  -e, --error ppm       m/z error (default: "10.0")
  -t, --thres (≥0.0)    exclusion threshold (default: "1.0")
  -n, --fold fold       number of precursor ions (default: "4.0")
  --inst                preserve original (instrument) ions
  -f, --fmt csv,tsv,ms2,mgf
                        output format (default: "csv")
  -h, --help            show this help message and exit

For macOS users, the executable files would be located at /Applications/MesMS/ by default.


  • It is recommended to set the mass error to 10 ppm. And for MS1 scans with resolution ≤ 30k, error < 10 ppm may cause performance loss.
  • The IPV would be generated automatically based on the Averagine model.

Input and Output

The software accepts .mes, .ms1/.ms2, and .raw files as input. For data in other formats, you can convert them into .mes and .ms1/.ms2 files.

The software outputs .csv, .tsv, .ms2, and .mgf files. The .csv and .tsv files are list of precursor ions without MS/MS spectrum peaks. The .ms2 and .mgf files contain both the precursors ions and MS/MS spectrum peaks, and can be used for peptide identification directly.