Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences.

Given an RNA (oligonucleotide) sequence and a charge state, the charged mass (including H+ adducts or losses), mass-to-charge ratio and molecular sum formula are computed. The sequence can include modifications (for information on valid notation see the NASequence 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 RNA sequences and charge for charge states. Alternatively, it can be read from a file (see parameter in) with the following format: An RNA 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 "ACGU: z=-2 m=1221.1951 m/z=610.5976 f=C38H46N15O26P3, z=-1 m=1222.2030 m/z=1222.2030 f=C38H47N15O26P3";
table produces a CSV-like table (using parameter separator to delimit fields) with the columns "sequence", "charge", "mass", "mass-to-charge" and "formula", and with one row per sequence and charge state;
mass_only writes only mass values (one line per sequence, values for different charge states separated by spaces);
mz_only writes only mass-to-charge ratios (one line per sequence, values for different charge states separated by spaces);
formula_only writes only sum formulas.

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

RNAMassCalculator -- Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_RNAMassCalculator.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  RNAMassCalculator <options>

Options (mandatory options marked with '*'):
  -in <file>               Input file with RNA sequences and optionally charge numbers (mutually exclusive to 'in_seq') (valid formats: 'txt')
  -in_seq <sequences>      List of RNA sequences (mutually exclusive to 'in')
  -out <file>              Output file; if empty, output is written to the screen (valid formats: 'txt')
  -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_only': mass values only, 'mz_only': m/z values only, 'formula_only': sum formula only)
                            (default: 'list') (valid: 'list', 'table', 'mass_only', 'mz_only', 'formula_only')
  -average_mass            Compute average (instead of monoisotopic) oligonucleotide masses
  -fragment_type <choice>  For what type of sequence/fragment the mass should be computed
                            (default: 'full') (valid: 'full', 'internal', '5-prime', '3-prime', 'a-B-ion', 'a-ion', 'b-ion', 'c-ion', 'd-ion', 'w-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

+RNAMassCalculatorCalculates masses, mass-to-charge ratios and sum formulas of RNA sequences

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'RNAMassCalculator'

in Input file with RNA sequences and optionally charge numbers (mutually exclusive to 'in_seq')input file*.txt

in_seq[] List of RNA sequences (mutually exclusive to 'in')

out Output file; if empty, output is written to the screenoutput file*.txt

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, 'formula_only': sum formula only)
list, table, mass_only, mz_only, formula_only

average_massfalse Compute average (instead of monoisotopic) oligonucleotide massestrue, false

fragment_typefull For what type of sequence/fragment the mass should be computed
full, internal, 5-prime, 3-prime, a-B-ion, a-ion, b-ion, c-ion, d-ion, w-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