SPECPLOT

Spectrum Generation


To generate a distinct spectrum, only the spectrum data and the peptide information are required.  The latter consists of a space-separated list of strings representing one or two peptide(s).  For example:

$ ./specplot --mgf specs_ms.mgf --spectrum 1 --peptide "[273.2]TDQDSQDSTYSFSS[214.2]" "SWTDQDSKDSTYS(M,16.0)SSTL"

poster_asms10_specplot.pdf - graphic illustration of specplot capabilities and parameters.

Will generate the associated representation in a 'png' file format of the first spectrum found within the input file. 

Different output formats such as 'eps' can be specified with the '--format' command-line option.  Here is a summary of relevant options:

  --pklbin FILE               Spectrum data (pklbin format)
  --mgf FILE                  Spectrum data (mgf format)
  --pkl FILE                  Spectrum data (pkl format)
  --mzxml FILE                Spectrum data (mzxml format)

  --aa FILE                   Amino acids file (txt format)
  --label FILE                Explicit labels [mass, height, type, order, charge]

  --spectrum INDEX            Spectrum (X) 1-based
  --spectrumscan INDEX        Spectrum scan (X)
  --spectruminfo STRING       Spectrum info
  --peptide STRING            Contiguous amino acid letters
  --annot FILE                Write annotations [mass, height, type, order, charge] to FILE
  --shift                     Apply mass shift
  --notitle                   Disables title generation
  --zoom NUMBER               Zoom factor

  --p FILE                    Parameters to read from file
  --format STRING             Image output format (png or eps)
  --outdir PATH               Output directory
  --prefix STRING             Output filename prefix
  --outfile FILE              Output filename (overrides prefix)
  --peakmasstol NUMBER        Amino acid peak mass tolerance
  --parentmasstol NUMBER      Parent mass tolerance

Missing parameters not documented in the command line help:

  --range X:Y                 Zoom spectrum to m/z range between m/z=X and m/z=Y
  --label FILE                Loads peak annotations [mass, height, type, order, charge] from FILE

Note: The generated annotation file can in turn be passed in as an argument to generate labels explicitly.  It follows the 'mgf' file format:

 $ ./specplot --mgf spectrum.1.0.txt --label spectrum.1.0.txt
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