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Gene Selkov, Jr. > Finnigan > uf-mzml


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uf-mzml - convert a Finnigan raw file to mzML


uf-mzml [options] <file>


  -a[ctivationMethod] <symbol>     specify ion activation method [CID by default]
  -c[entroids]                     write peak centroids instead of scan profiles where possible
  -r[ange] <from> .. <to>          write only scans with numbers between <from> and <to>
  -q[uiet]                         suppress the instrument error messages
  -u[nencoded]                     render the data unencoded (in decimal encoding)
  -s[tructure]                     output just the XML structure of the file (without the data)
  <file>                           input file



Prints a brief help message and exits.

-a[ctivationMethod] <symbol>

Since the native storage location of the data element corresponding to the activation method is unknown at this time, the required mzML activation attribute is set to 'collision-induced dissociation' by default. It is a valid assumption in most Orbitrap experiments. The -a option overrides the default value. The symbol specified on the command line is simply copied into the activation element, provided it exists in the mzML controlled vocabulary. A small fragment of the vocabulary included in uf-mzml consists of:

  'collision-induced dissociation'
  'surface-induced dissociation'
  'electron capture dissociation'
  'electron transfer dissociation'
  'multiphoton dissociation'
  'infrared multiphoton dissociation'

Prefer centroids to raw profiles.

Note: presently, uf-mzml does not do its own centroiding. If a scan contains no centroid data, the profile is written out.

-r[ange] <from:0+n> .. <to:0+n>

Selects a range of scans to process.

Note: in order to establish valid references within the mzXML file, the first scan in the selected range has be a full MS1 scan. Otherwise, the program will exit with the following message:

  C<Range error: cannot form valid mzML starting with the dependent scan ###>

To determine the appropriate range of scans, list all scans in the file using uf-trailer.


Suppress the instrument error messages stored in the input file. Without this option, the error messages will be printed to STDERR.


Dump the contents of each binary element in human-readable decimal encoding


Do not output scan data, preserving the overall structure of the XML document. This option is useful in troubleshooting the structure of the output file and its metadata.


Finnigan::Scan Finnigan::Profile Finnigan::ProfileChunk uf-trailer


 uf-mzml sample.raw > sample.mzML

  (convert the entire file, using profiles from those scans where both
  profiles and centroids are present and centroids where there are no

 uf-mzml -c sample.raw > sample.mzML

  (convert the entire file, extracting precomputed centroids from
  every scancontaining centroids; where there are no centroids, the
  profile will be used)

 uf-mzxml -c -r 350 .. 352 20070522_NH_Orbi2_HelaEpo_05.RAW > sample.mzML

  (extract peak centroids from scans 350 through 352)

 uf-mzml -a "electron transfer dissociation" sample.raw > sample.mzML

  (override the default dissociation method)
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