NAME

uf-mzml - convert a Finnigan raw file to mzML

SYNOPSIS

uf-mzml [options] <file>

 Options:

  -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

OPTIONS

-help

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'
  'photodissociation'
  'multiphoton dissociation'
  'infrared multiphoton dissociation'

-c[entroids]

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.

-q[uiet]

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

-u[nencoded]

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

-s[tructure]

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.

SEE ALSO

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

EXAMPLES

 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
  profiles)

 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)