VIPER 3.49 B467 467

VIPER (Visual Inspection of Peak/Elution Relationships) can be used to visualize and characterize the features detected during LC-MS analyses. It is primarily intended for processing deisotoped data from high mass measurement accuracy instruments (e.

VIPER 3.49 B467 467

VIPER (Visual Inspection of Peak/Elution Relationships) can be used to visualize and characterize the features detected during LC-MS analyses. It is primarily intended for processing deisotoped data from high mass measurement accuracy instruments (e.g. FT, TOF, or Orbitrap) and comparing the features found to a list of expected peptides (aka mass and time (MT) tags), as practiced by the AMT tag approach (see Zimmer, Monroe, Qian, & Smith, Mass Spec Reviews, 2006, 25, 450-482).

The software allows one to display the data as a two-dimensional plot of spectrum number (i.e. elution time) vs. mass. It can read MS data from several file formats: .PEK, .CSV (Decon2LS format), .mzXML, and .mzData. See the Readme.txt file installed with VIPER for additional details on the various file formats. VIPER runs on Windows computers and requires Microsoft Access be installed to create and edit the MT tag databases. In order to view mass spectra from raw data files (e.g. ThermoElectron (i.e. Finnigan style) .Raw files), you will also need to install ICR-2LS found above.

The "Data Extraction and Analysis for LC-MS Based Proteomics" sessions at the 2007 and 2008 US HUPO conferences discussed the use of VIPER for processing example LC-MS datasets and matching to an AMT tag database. PDF files of the slides presented are available for download as a 5 MB PDF file (2007) and a 6.5 MB PDF file (2008). See also the Open Source Tools for the Accurate Mass and Time (AMT) Tag Proteomics Pipeline poster presented by Navdeep Jaitly at ASMS 2006. This poster presents an overview of VIPER and its interactions with other proteomics software. Lastly, a help file in PowerPoint format is also available, but keep in mind that this file is fairly out-of-date on several of the slides. Note also that the MTDB Creator software can be used to generate AMT tag databases in the Microsoft Access file format.
Release notes: New Release
TE New version of STAC that defaults to have drift time alignment turned off
TE Optionally enable this via the "Use Drift Time Alignment" option in the Search MT DB window
TE Corresponding .Ini file option is STACAlignsDriftTime in the ExpandedPreferences section
TE Fixed bug on the Tolerance Refinement form that computed slightly shifted Drift Time errors when using UMC class stats
[ VIPER full changelog ]

   



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