NCRR Proteomics Resource at PNNL

VIPER

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 Lastly, a help file in PowerPoint format is also available, but keep in mind that this file is fairly out-of-date on several of the slides.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.

The source code for VIPER is fairly large, but includes a reasonable amount of in-code documentation. If you make any improvements to the algorithms used by VIPER, we would encourage you to send the updated code to us at proteomics@pnl.gov

Download Software Tool

Download Source Code

Version	v3.43.380	Requirements	Microsoft VB6 Runtime (included with installer)
Date Updated	November 5, 2007	File Size (Software Tool)	11.8 MB (ZIP)
Registration Required	No	File size (Source Code)	7.2 MB (ZIP)
Developers	Matthew Monroe; Nikola Tolic
Comments	See the complete Revision History for a history of changes

Acknowledgment

All publications that result from the use of this software should include this statement:

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

VIPER Feature Tour

Find out what is in VIPER. Take the feature tour to learn about some of the top features of this product.

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Provides a Steps menu to guide users through a typical analysis of deisotoped LC-MS data. Default values are provided if the input of parameters is required. Peak matching can be carried out through an automated process once processing steps and parameters are defined in an .ini file. Ini files can be set up for different instruments and for 14N/15N or 16O/18O pairs.

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Allows visualization of LC-MS mass spectra from raw data files and peaks lists from ICR-2LS/ Decon2LS through 2D plots (monoisotopic mass vs. scan number) and call ICR-2LS to display mass spectra from raw data files. Also allows viewing total ion chromatograms (TICs), selected ion chromatograms (SICs) and base peak ion (BPI) plots.

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Allows data filtering through the use of various filtering criteria (such as isotopic fit, m/z range, mass range, charge state range)

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Finds features (i.e. Unique Mass Classes, UMCs) from MS data, allows a charge state view and the capability to zoom-in to view features and feature details (i.e. median mass, elution time, abundance).

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Optionally, paired features (e.g 16O/ 18O pairs) can also be found.

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Matches UMCs to potential mass and time (PMT) tags from an organism specific PMT tag database.

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Align elution time of UMCs to the Normalized Elution Times (NETs) of peptides in a given PMT tag database to find optimal alignment to give the most matches. Current version of VIPER uses linear regression for NET alignment, however the upcoming version will utilize a MS Warp algorithm to carry out NET alignment.

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Matches features to PMT tags once again after completion of feature NET alignment. If a given feature matches more than one PMT tag, a Spatially Localized Confidence (SLiC) score is used to measure the uniqueness of a match. Mass error histograms of mass difference between PMT tag mass and feature mass are generated.

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Carries out a mass calibration refinement (i.e. adjust masses of features) by using the peak in mass error plot or by using MS Warp (note: MS Warp will be utilized in the next available version). Feature matching is repeated after mass calibration using final search tolerances.