OpenMS
MassCalculator

Calculates masses and mass-to-charge ratios of peptide sequences.

Given a peptide sequence and a charge state, the charged mass (including H+ adducts) and the mass-to-charge ratio are computed. The peptide sequence can include modifications (for information on valid notation see the AASequence class documentation). Neutral masses can be computed by using "0" as charge state.

Input can be given directly as values of the parameters: in_seq for peptide sequences and charge for charge states. Alternatively, it can be read from a file (see parameter in) with the following format: A peptide sequence at the beginning of each line, optionally followed by any number of charge states. Whitespace, commas or semicolons can de used to delimit the different items. Parts of the input that cannot be understood will be skipped. If charge states are given in the input file as well as via the charge parameter, results are returned for the union of both sets of charge states.

Output can be written to a file or to the screen (see parameter out). Results for different charge states are always ordered from lowest to highest charge. A number of different output formats are available via the parameter format:

  • list writes a human-readable list of the form "ABCDEF: z=1 m=566.192 m/z=566.192, z=2 m=567.199 m/z=283.599";
  • table produces a CSV-like table (using parameter separator to delimit fields) with the columns "peptide", "charge", "mass", and "mass-to-charge", and with one row per peptide and charge state;
  • mass_only writes only mass values (one line per peptide, values for different charge states separated by spaces);
  • mz_only writes only mass-to-charge ratios (one line per peptide, values for different charge states separated by spaces).

The command line parameters of this tool are:

Error: Residue::getResidueTypeName - residue type has no name. The developer should add a residue name to Residue.cpp
Error: Residue::getResidueTypeName - residue type has no name. The developer should add a residue name to Residue.cpp

MassCalculator -- Calculates masses and mass-to-charge ratios of peptide sequences
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MassCalculator.html
Version: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  MassCalculator <options>

Options (mandatory options marked with '*'):
  -in <file>                   Input file with peptide sequences and optionally charge numbers (mutually excl
                               usive to 'in_seq') (valid formats: 'tsv')
  -in_seq <peptide_sequences>  List of peptide sequences (mutually exclusive to 'in')
  -out <file>                  Output file; if empty, output is written to the screen (valid formats: 'csv')
  -charge <numbers>            List of charge states; required if 'in_seq' is given (default: '[0]')
  -format <choice>             Output format ('list': human-readable list, 'table': CSV-like table, 'mass_onl
                               y': mass values only, 'mz_only': m/z values only)
                                (default: 'list') (valid: 'list', 'table', 'mass_only', 'mz_only')
  -average_mass                Compute average (instead of monoisotopic) peptide masses
  -fragment_type <choice>      For what type of sequence/fragment the mass should be computed
                                (default: 'full') (valid: 'full', 'internal', 'N-terminal', 'C-terminal', 
                               'a-ion', 'b-ion', 'c-ion', 'x-ion', 'y-ion', 'z-ion')
  -separator <sep>             Field separator for 'table' output format; by default, the 'tab' character is 
                               used
                               
Common TOPP options:
  -ini <file>                  Use the given TOPP INI file
  -threads <n>                 Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>            Writes the default configuration file
  --help                       Shows options
  --helphelp                   Shows all options (including advanced)

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+MassCalculatorCalculates masses and mass-to-charge ratios of peptide sequences
version3.2.0-pre-nightly-2024-07-21 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MassCalculator'
in Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')input file*.tsv
in_seq[] List of peptide sequences (mutually exclusive to 'in')
out Output file; if empty, output is written to the screenoutput file*.csv
charge[0] List of charge states; required if 'in_seq' is given
formatlist Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)
list, table, mass_only, mz_only
average_massfalse Compute average (instead of monoisotopic) peptide massestrue, false
fragment_typefull For what type of sequence/fragment the mass should be computed
full, internal, N-terminal, C-terminal, a-ion, b-ion, c-ion, x-ion, y-ion, z-ion
separator Field separator for 'table' output format; by default, the 'tab' character is used
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue, false
forcefalse Overrides tool-specific checkstrue, false
testfalse Enables the test mode (needed for internal use only)true, false