uf-scan - examine scan data in a single MS scan
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]
Print a brief help message and exits.
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.
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.
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.
Gives the number of a single scan to process
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.
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.
uf-scan -p -n 1 sample.raw
uf-scan -ep -n 1 sample.raw
uf-scan -pv -n 1 sample.raw
uf-scan -pvz -n 1 sample.raw
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.
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.
uf-scan -d -p -n 18588 sample.raw | grep fudge | cut -f 5