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)