Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

Table 3 Results of processing three LC-MS datasets using Decon2LS

Dataset	MS scans in dataset	peaks in dataset	isotopic patterns found	LC-MS features	Processing time
ShewFed028_LTQFT_1_29May05_Andro_0505-02	5100	2,967,743	106,150	6670	22 min
Caulo_084_run3_03Nov06_Andro_06-06-12	2950	5,797,366	76,567	5036	1 hr 08 min
EIF_NAF_CF_Cys1_21Oct06_OWL_06-08-02	3312	1,556,780	34,205	2817	18 min

This table lists the numbers of scans in the LC-MS datasets, the numbers of peaks found by the peak detection algorithm, the number of isotopic patterns found in the peaks and the number of LC features found by grouping together the isotopic patterns using retention time. The processing time was larger for the in-house FTICR dataset because the dataset was larger (~8 Gb) than the other two datasets, which were smaller because the Thermo Fisher acquisition software, Xcalibur, sets a minimum intensity threshold.

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