NAME

uf-mzxml - convert a Finnigan raw file to mzXML

SYNOPSIS

uf-mzxml [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>
 <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 mzXML attribute is set to 'CID' (Collision-Induced Dissociation). 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 activationMethod attribute of the precursorMz element, and there is no constraint on what it can be.

-c[entroids]

Prefer centroids to raw profiles.

Note: presently, uf-mzxml 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 form the nested structure of dependent scans required in mzXML, 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 mzXML 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.

SEE ALSO

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

EXAMPLE

uf-mzxml -c -r 350 .. 352 20070522_NH_Orbi2_HelaEpo_05.RAW > test.xml

 (extract peak centroids from scans 350 through 352)