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Table 1 Access Efficiency for Open and Proprietary Mass Spectrometry Data Files.

From: multiplierz: an extensible API based desktop environment for proteomics data analysis

    mean sd
Random Access   XDK (RAW) 1.81 0.01
(milliseconds)   mzAPI (RAW) 16.11 2.23
   mzAPI (WIFF) 216.10 8.58
RIC Generation GUI mzAPI (RAW) 0.58 0.03
(milliseconds)   Insilicos (mzXML) 12.17 1.93
  Script mzAPI (RAW) 0.39 0.01
   InSilicoSpectro (mzXML) 15.68 0.06
   XCMS (mzXML) 37.46 4.74
  1. Benchmarks for data access efficiency as determined for random scan access (orange fields) and generation of RICs (green fields). Three files were used: a RAW file acquired in data-dependent mode on an Orbitrap (ThermoFisher Scientific) with MS scans in profile mode and MS/MS scans in centroid mode; a WIFF file acquired in information dependent mode on a QSTAR Elite (MDS/Sciex) with all scans in profile mode; and a mzXML file generated using TPP (version 3.2) with the aforementioned RAW file as the source. For comparison of random access times a common single script was used to access both the RAW and WIFF file, by selecting 1000 scan times at random and that uniformly span the acquisition range. An equivalent process was implemented in C++ using the ThermoFisher XDK. For RIC generation in GUI mode (meaning that the resulting RIC is displayed by the software in an interactively accessible window) a script to animate the InsilicosViewer V1.5.1 was compared against a similar .mz script. For the non-GUI scenario we compared an R (version 1.12.1) script using the XCMS library as well as a Perl script using the InSilicoSpectro library (version 1.3.19) to another .mz script. The .mz scripts, R script, Perl script and C++ program are all available in Additional File 1. All measurements were repeated N = 20 times.