NAME

uf-scan - examine scan data in a single MS scan

SYNOPSIS

uf-scan [options] file

Options:

 -d[ump]                       dump the packet header (-d); dump the header and the profile (-dp)
 -e[xtract]                    extract the entire scan data as a binary chunk
 -l[ist]                       list the called peaks [required]
 -p[rofile]                    print the scan profile as a 2-column table [required]
 -plot                         plot the profile (along with the called peaks, if available) [required]
 -v                            convert f -> M/z [requires: -p]
 -z                            add empty bins [requires: -p]
 -n[umber] <n:+i>              select scan number <n> [required]
 -mz <low:+n> .. <high:+n>     limit the plot to the range of M/z values between <low> and <high> [requires: -plot]
 <file>                        input file [required]

OPTIONS

-help

Print a brief help message and exits.

-l[ist]

Get the peak list from the scan number -n, if they are available. If the called peaks are not present, uf-scan will print a message to that effect and exit.

-p[rofile]

Prints the scan profile for scan number -n, if it is available. If the profile is not present, uf-scan will print a message to that effect and exit.

-plot

This option generates an R script to plot the profile. Prints the scan profile for scan number -n, if it is available. If the profile is not present, uf-scan will print a message to that effect and exit.

-n[umber]

Gives the number of a single scan to process

-e[xtract]

Used with either -l or -p, this option option clips the binary data chunk corresponding to either the peak list or to the scan profile and sends it to STDOUT.

DESCRIPTION

uf-scan can be used to list or plot the scan data for a single scan. The -profile option instructs uf-scan to print the profile data, the -list option lists the peaks, and the -plot option writes an R script to plot the profile and peak centroids, if both kinds of data are present in the raw file, or just the profile if the centroids are not present.

Options -profile, -list and -plot are mutually exclusive.

To convert the raw scan data into M/z values, use the -v option.

Option -z fills the gaps between the profile peaks with zeroes, to create a continuous table.

SEE ALSO

Finnigan::PacketHeader

Finingan::Profile

Finingan::Peaks

Finnigan::Scan

uf-mzxml

EXAMPLES

Print all raw profile bins in the 1st scan:

uf-scan -p -n 1 sample.raw

Extracts the entire scan profile in the binary form:

uf-scan -ep -n 1 sample.raw

Same as above, except the bin values will be converted into M/z:

uf-scan -pv -n 1 sample.raw

Same as above, but in addition, all empty bins are wirtten out as well:

uf-scan -pvz -n 1 sample.raw

Print the list of centroids in the 1st scan:

uf-scan -l -n 1 sample.raw

Note that uf-scan does not calculate the peak centroids from the profile; it only lists the existing centroids if they are present.

This command will call R to plot the profile in the given range of M/z values:

uf-scan -plot -n 1 -mz 445.0 .. 445.2 sample.raw | R --vanilla --slave > plot.eps

If called peaks are present, they will be shown as dots on the graph.

To see the amount of correction applied to each bin in a scan:

uf-scan -d -p -n 18588 sample.raw | grep fudge | cut -f 5