View on
Gene Selkov, Jr. > Finnigan > uf-scan-light


Annotate this POD


New  1
Open  0
View/Report Bugs


uf-scan-light - list the profile or centroids in a single MS scan


uf-scan-light [options] file


  -l[ist]                            list the called peaks [required]
  -p[rofile]                         print the scan profile as a 2-column table [required]
  -b[ookends] <n:+i>                 add <n> empty bins on both sides of each profile chunk [requires: -p]
  -n[umber] <n:+i>                   select scan number <n> [required]
  -mz                                list just the M/z values
  <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-light 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-light will print a message to that effect and exit.


Gives the number of a single scan to process


Sets the number of empty bins to add prepend and append to each profile chunk. Doing so can enhance the appearance of peak shapes rendered on simple plots when the profiles are filtered. Threshold filtering removes the bases of detected peaks as well, so this is a primitive way of reconstructing them.


uf-scan-light can be used to list the scan data for a single scan. Unlike uf-scan, it is based on a lightweight version of scan data decoder, Finnigan::Scan, which does not preserve the location and type data of decoded elements and therefore cannot generate detailed data dumps. But there is one thing uf-scan-light does that uf-scan does not: it mimics the manner in which Thermo-derived tools assign bin values in profile mode and it can insert stretches of empty bins on both sides of each profile peak, in the same way as they do it. Setting the value of the -bookends option to 4 results in the same output as that of readw or msconvert.

Also, uf-scan-light does not output the raw profiles. It automatically converts frequency values to M/z.

The -profile option instructs uf-scan-light to print the profile data. The -list option lists the peaks.

Options -profile and -list are mutually exclusive.

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

Option -bookends adds the specified number of empty bins to each side of a profile chunk. If the gap is smaller than 2x the number of bookend bins, it is completely zeroed out.








Print converted profile bins (M/z values) in the 1st scan:
 uf-scan-light -p -n 1 sample.raw
Print converted profile bins in the 1st scan and add four-bin 'bookends' to make the output look like Thermo's:
 uf-scan-light -p -n 1 -b 4 sample.raw
Print the list of centroids in the 1st scan:
 uf-scan-light -l -n 1 sample.raw

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

syntax highlighting: