Biological MS Data and Software Distribution Center 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 Lastly, a help file in PowerPoint format is also available, but keep in mind that this file is fairly out-of-date on several of the slides.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  

Software Details
Version v3.44.394 Requirements Microsoft VB6 Runtime (included with installer)
Date Updated June 11, 2008 File Size (Software Tool) 11.9 MB (ZIP)
Registration Required No File size (Source Code) 7.8 MB (ZIP)
Developers Matthew Monroe; Nikola Tolic
Comments See the complete Revision History for a history of changes

 

Acknowledgment

All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:

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

Easy to Use Steps Menu

Steps Menu

(+) View larger

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.

 

Visualization of mass spectra and ICR-2LS / Decon2LS peak lists

Mass Spectra

(+) View larger

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.

 

Data Filtering

Data Filter Window

(+) View larger

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

 

Feature Finding

Zoomed Charge State View

(+) View larger

Finds LC-MS 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).

 

Finding Isotopic Paired Features

Isotopic Pairs Features

(+) View larger

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

 

Selection of peptide database

Connect to Database Window

(+) View larger

Matches LC-MS Features (UMCs) to accurate mass and time (AMT) tags from an organism specific AMT tag database

 

Mass and NET Alignment with LCMSWarp

LCMSWarp Window

(+) View larger

Align elution time of LC-MS Features to the Normalized Elution Times (NETs) of peptides in a given AMT tag database to find optimal alignment to give the most matches. VIPER now supports the LCMSWarp algorithm that allows for non-linear NET alignment and simultaneous mass and NET alignment in one step.

 

Mass Error Histogram

Mass Error Histogram

(+) View larger

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

 

Mass Calibration Refinement

Mass Calibration Refinement Window

(+) View larger

Carries out a mass calibration refinement (i.e. adjust masses of features) by using the peak in the mass error plot. Feature matching is repeated after mass calibration using final search tolerances.