DTA Generator
DTA Generator creates .dta input files for the Open Mass Spectrometry Search Algorithm (OMSSA) directly from Thermo Scientific .raw LC-MS/MS data files. For each fragmentation spectrum, DTA Generator first attempts to determine the precursor charge state using the information recorded in the scan header. If this information is available, only a single .dta file is written using that precursor charge. If it is not available (could not be determined by the instrument firmware), a .dta file is generated for every charge state in a user-specified range. The precursor [M + H]+ value is written with its corresponding charge state, followed by every centroid m/z and intensity pair from the MS2 scan. DTA Generator takes multiple input .raw files, automatically distinguishes between CAD- and ETD-generated spectra, allows the user to specify which spectral features should be removed (i.e., precursor, charge-reduced precursor(s), and/or neutral losses from charge-reduced precursors), and generates either individual .dta files or merges 10,000 .dta files into batch text files (for searching with OMSSA).
The software supports three different ETD spectral pre-processing options: (1) removal of the precursor—all peaks ± 3.1 m/z from the precursor m/z; (2) removal of those charge-reduced precursor cations that were the result of ETnoD—all peaks ± 3.1 m/z from the charge-reduced precursor m/z for each charge state from +1 to the precursor charge state −1; and (3) removal of those peaks that were the result of neutral losses from charge-reduced precursors—all peaks −60 Da (scaled to charge) to the charge-reduced precursor m/z for each charge state from +1 to the precursor charge state − 1.
System Requirements
- Microsoft Windows operating system
- Thermo Scientific Xcalibur 2.0 or later
- Microsoft .NET Framework version 2.0
If you use this software in a publication, please cite:
Good DM, Wenger CD, McAlister GC, Bai DL, Hunt DF, and Coon JJ. Post-Acquisition ETD Spectral Processing for Increased Peptide Identifications. Journal of the American Society for Mass Spectrometry. e-published 14 March 2009.