• input
• sequence
• spectrum
• help

[no datafile opened]

[no configuration file opened]

SOS v2.0

Usage

• input
  Load datafile (mass - intensities from centroid spectra) and configuration file (text file). The configuration file will be displayed.
  An example spectrum is available, as well as standard DNA and RNA configuration files that can be loaded.
  Custom configuration files with user defined modified residues can be uploaded.
  Note that all uploaded data will reside in your browser's memory only. No data is tranferred to any kind of cloud or servers.
• sequence
  Panels will show up when a configuration file is loaded
  The number of panels (maximum 8) depend on the number of residues defined in the configuration file
  Select the ion type and charge
  Type the sequence in the input field or click on the panels
  The m/z axis displays the calculated value for the next residue
  The tick mark spacing on the m/z axis is 1u
  Number at the top right corner of the panels indicate the intensity of the highest peak displayed in all the panels
• spectrum
  A spectrum is shown after reading input data and initializing the sequence window
• help
  It's what you are reading now.

Data files

• must contain m/z intentity records delimited by tabs (centroid data)
• lines starting with a colon are considered to be remarks and are ignored

Configuration files

• element masses should come first
• number of masses should correspond to number of elements
• use one-character codes for elements (e.g., replace Cl by L) and for residues
• the order of the panels corresponds to the order in the configuration file
• the a-B ion furan is calculated from the fist nucleotide in the 'symbols=' sentence
• lines starting with a colon are considered to be remarks and are ignored
• see figure below for composition of nucleotide moieties and for an example configuration file

download: [DNA configuration file] [RNA configuration file]

:
:example configuration file for DNA
:
:element masses
:
elements=C|H|N|O|P
elmass=12.0000|1.00782|14.00307|15.99491|30.97376
:
:end groups
:
end3=OH
end5=HO
:
:residues
:
symbols=A|C|G|T
bases=C5H4N5|C4H4N3O|C5H4N5O|C5H5N2O2
sugars=C5H7O|C5H7O|C5H7O|C5H7O
link1=O|O|O|O
link2=PO2H|PO2H|PO2H|PO2H
link3=O|O|O|O