.raw to .dta conversion

[tr...@york.ac.uk]

Hello,
I have data-dependent ms2 .raw files, collected under a +APCI method
using Xcalibur 2.0 on an LCQ or a LTQ-FT. I want to convert these
to .dta files. I think Bioworks can do this, but I don't have this as
we don't do proteomics. Also, I understand .dta files are usually
extracted from +esi runs; I don't know if +APCI runs will present a
problem. Finally, I obviously want to create .dta files from both LCQ
and LTQ-FT systems (we have both machines in-house).

Is there a utility for doing this? I see I have a program in

xcalibur\system\programs

called called extract_msn.exe, but I have no idea on how to use it and
there is no help file on doing this in any of the xcalibur
documentation I have.

thanks
Tony

[rlmobil]

Hi Tony,

see below and simply try with APCI data.

Good luck
Rainer

C:\Xcalibur\System\Programs>extract_msn
EXTRACT_MSN usage: extract_msn [options] [datafile]
options = -Fnum where num is an INT specifying the first scan

-Lnum where num is an INT specifying the last scan

-Bnum where num is a FLOAT specifying the bottom MW for
datafilecreation

-Tnum where num is a FLOAT specifying the top MW for
datafile creation

-Mnum where num is a FLOAT specifying the precursor mass
tolerance for grouping (default=1.4)

-Snum where num is an INT specifying the number of allowed
different intermediate scans for grouping. (default=1)

-Cnum where num is an INT specifying the charge state to use

-Gnum where num is an INT specifying the minimum # of related
grouped scans needed for a .dta file (default=2)

-Inum where num is an INT specifying the minimum # of ions
needed for a .dta file (default=0)

-Rnum where num is a FLOAT specifying the minimum signal-to-noise
value needed for a peak to be written to a .dta file
(default=3)

-rnum where num is an INT specifying the minimum number of
major peaks (peaks above S/N threshold) needed for a .dta file
(default=5)

-Dstring where string is a path name

-Ystring where string is a subsequence

-Z Controls whether the zta files are written

-K Controls whether the charge calculations are performed

-Ustring where string is the path of a template file
[Default name is chgstate.tpl]

-Acontrolstring containing any of the options
T: use template F: use discrete Fourier transform
E: use Eng's algorithm H: use scan header
M: use MSMS count
O: override header charge state
S: create summary file L: create log file
D: create both files C: create MSMS count file
A: find CS even for nonzero headers
tfehm: include algorithm output in summary file even if not called
[NOTE: This version of the program has a default string of -AHTFEMAOSC,
but if -A option is used all desired parameters must be specified]

-H print this information

If lcq_dta.exclude present, will ignore list of ions in exclude list.
Format of lcq_dta.exclude: mass tolerance on 1st line
precursor masses on subsequent lines

C:\Xcalibur\System\Programs>