OpenMS
2.5.0
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Calculates masses and mass-to-charge ratios of RNA sequences.
Given an RNA (oligonucleotide) sequence and a charge state, the charged mass (including H+ adducts or losses) and the mass-to-charge ratio 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 "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 "sequence", "charge", "mass", and "mass-to-charge", 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).The command line parameters of this tool are:
RNAMassCalculator -- Calculates masses and mass-to-charge ratios of RNA sequences Full documentation: http://www.openms.de/documentation/UTILS_RNAMassCalculator.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. 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) (default: 'list' valid: 'list', 'table', 'mass_only', 'mz_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 UTIL 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: