PeakView: The Complete Spectral Analysis Software Solution

• Flexible platform enables a range of data exploration alternatives with the addition of several micro-applications:
  • SWATH® Acquisition: intuitive interface for comprehensive quantitative proteomics
  • Bio Took Kit Software: tools for the characterization of biomolecules, including MW determination and peptide sequence tagging
  • MasterView™ Software: reliable and easy data processing
  • Peptide Quantification Micro Application (PQMA): data analysis tool for the quantitation of peptides using MS data. Links to MarkerView for metabolite and biomarker profiling applications
• New in PeakView Software v2.1
  • Support for nominal mass (QTRAP) as well as accurate mass (TripleTOF data)
  • Support for optional detectors such as UV, DAD, ADC
• Intuitive software features enable data investigation by showing mass differences between peaks, generating background subtracted spectra, merging refined spectra, or creating contour plots
• Spectra from multiple samples can be viewed simultaneously in a single window as overlaid chromatograms or heat maps for quick and easy qualitative review and comparison
• Processing parameters can be applied across large sample sets saving time during data processing and review
• An information dependent acquisition (DIA) viewer presents data in a convenient graphic and tabular view with specialized tools to filter data based on criteria such as quality, mass defect, and isotopic pattern.
• Specialized tools such as the Formula Finder and Structure Elucidation enable detailed investigation and characterization at the molecular level
• Functionality for working with MS/MS^ALL data (precursors of all products) enables visualization of the entire fragmentation space in a single plot as well as instant comprehension of common fragments and neutral losses.

Formula Finder: Formula Finder is an enhanced elemental formula calculator for small molecule analysis. It quickly calculates all possible elemental formula for detected masses using both accurate mass and isotope distribution. The software will use MS/MS data when available to confirm the identity of the most-likely candidates, while applying chemical logic to filter out unlikely candidates. Interactive re-calibration tools based on common background ions or experimentally-determined fragment masses ensure highest accuracy mass reporting.

Figure 1: The Formula Finder tool.

Structure elucidation: PeakView Software links the masses of ions to structures (saved as .MOL files) to help identify and characterize compounds, explore possible sites for biotransformations, and provide insights into fragmentation mechanisms.  Once a structure is linked to a spectrum, parts of the structure can be selected to determine if there is a corresponding peak. Matching compositions, substructures, and mass peaks can all be observed. To show more complex fragmentation pathways, the fragment options can be modified.  Additionally, the structures can be modified to explore the fragmentation of related compounds.

Figure 2: Structure of buspirone determined by MS/MS data.

XIC Manager: The XIC Manager allows you to manage large lists of compounds and perform automatic, extracted-ion-chromatogram (XIC) calculations and other peak-finding operations. It consists of a tabled list of masses or formulas to generate XICs, as well as a review pane for XIC results including any library search results. Information such as intensity, retention time, library search results (if applicable), and confidence is displayed in the table. Each column of the result table can be sorted, filtered to display specific data, or searched for specific information.

Figure 3: Result Table using XIC Manager.

Protein Quantitation MicroApp:  The Protein Quantitation 1.0 MicroApp is a PeakView Software plug-in that provides a seamless transition from ProteinPilot™ Software version 4.0 to MarkerView™ Software version 1.2.1 for profiling peptides and proteins across multiple samples using MS-peak extracted ion chromatograms (XIC) for quantitation. The tool allows selection of proteins and peptides from ProteinPilot Software group files, extraction of MS peak areas, and data export to MarkerView Software. Once in MarkerView Software, the data can be analyzed using statistical analysis tools to determine groups of similarly-behaving samples, proteins or peptides, outliers, and other relationships between peaks that can lead to biological discoveries. The Protein Quantitation MicroApp is a free download and requires ProteinPilot Software version 4.0, PeakView Software version 1.1.1 and MarkerView Software version 1.2.1.