VIPER (Visual Inspection of Peak/Elution Relationships)

Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract VIPER (Visual Inspection of Peak/Elution Relationships) is an advanced software package developed initially to support high-throughput peptide identification in the accurate mass and time (AMT) tag approach to high-throughput proteomics.

This approach is similar to ‘shotgun’ proteomics approaches in that proteins are first enzymatically cleaved into peptide fragments and then analyzed by liquid chromatography-tandem mass spectrometry (LC- MS/MS) to identify peptides using conventional software tools, such as SEQUEST (see G6G Abstract Number 20285), Mascot (see G6G Abstract Number 20087) or X!Tandem.

However, unlike shotgun approaches, the results from these initial analyses are stored in a reference database in the form of mass and (LC elution) time (MT) tags.

Each tag serves as a unique 2D marker for subsequent identifications of that particular peptide by high-resolution, high mass accuracy LC-MS (e.g. Fourier transform ion cyclotron resonance).

The LC-MS data are first processed using another PNNL developed software package called Decon2LS that uses a version of the THRASH algorithm to detect features (and their monoisotopic masses) in the individual mass spectra.

VIPER then processes collections of MS features (e.g. as found using Decon2LS) across elution time to identify unique ‘LC-MS features,’ and also calibrates elution times, refines the mass calibration and matches the LC-MS features to mass and (elution) time tags in a reference database.

The identified LC-MS features and the peptide/protein identifications can then be exported for further analysis using programs such as Microsoft Excel or Microsoft Access.

VIPER features/capabilities include:

1) Easy to Use Steps Menu --

VIPER 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.

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

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.

3) Data Filtering --

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

4) Feature Finding --

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).

5) Finding Isotopic Paired Features --

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

6) Selection of peptide database --

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

7) Mass and NET Alignment with LCMSWarp --

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.

Note: The LCMSWarp algorithm is described in Jaitly et al. 2006. Analytical Chemistry 78(21):7397-7409.

8) Mass Error Histogram --

Matches features to AMT tags once again after the 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.

9) Mass Calibration Refinement --

VIPER 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.

System Requirements

VIPER runs on Windows computers and requires Microsoft Access be installed to create and edit the MT tag databases.

Manufacturer

Manufacturer Web Site VIPER

Price Contact manufacturer.

G6G Abstract Number 20382

G6G Manufacturer Number 104020