In addition to the libraries, ProteoWizard distributes a number of applications. Many of these operate across Windows, Linux and Macintosh. Because of our reliance upon vendor libraries, some funcionality is only available on Windows. For example, reading vendor-data files. For command-line tools, running the program with no arguments will print usage information.
| WinOnly GUI Tools | |
|---|---|
| MSConvertGUI | interactive version of the msconvert tool for converting mass spec data files to various formats (Windows only) |
| SeeMS | interactive viewer for mass spec data files (Windows only) |
| Skyline | interactive application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM) methods and analyzing the resulting mass spectrometer data. (Windows only) |
| Topograph | interactive application for working with metabolic labeling and protein metabolism experiments. (Windows only) |
| General Information | |
| Filters | Information on the data filters and transformations provided by the ProteoWizard library, as used in msaccess, msconvert and other tools |
| Command-Line Tools | |
| chainsaw | peptide digest program, takes in sequence files, outputs peptides, masses, etc. |
| idConvert | Reads diverse peptide identification formats and outputs to mzIdentML (or other things) |
| msaccess | command line access to mass spec data files, including spectrum binary data and metadata, selected ion chromatograms, and pseudo-2D gel image creation | msbenchmark | ? |
| msconvert | general data format conversion tool |
| msdiff | comparison of two data files, for validation of conversion and preprocessing |
| msdir | ? |
| msistats | ? |
| mspicture | command line pseudo-2D gel image creation with mapped peptide ID info |
| mscat | exports data from a variety of formats into 4 column text format |
| peakaboo | ? |
| pepcat | ? |
| pepsum | ? |
| qtofpeakpicker | peak detection in Q-TOF (quadrupole time-of-flight) raw data |
| sldout | ? |
| ThermoRawMetaDump | extracts methods, tunes, and headers from RAW files as human-readable text. (Windows only) |
| txt2mzml | converts data from 4 column format to mzML |
| Tools for ProteoWizard Testing | |
| These are mostly for developers to make sure that they haven't broken anything | |
| hello_analyzer | ? |
| hello_analyzer_2 | ? |
| hello_msdata | ? |
| hello_ramp | ? |
| write_example_files | ? |
| write_mzid_example_files | ? |
| write_proteome_example_files | ? |
| write_traml_example_files | ? |