PeakView® Software
PeakView® Software is a stand-alone software application for the qualitative review of LC/MS and MS/MS data for the TripleTOF™ 5600 System. The software allows for exploring and interpreting mass spectral data with special tools for processing accurate mass data, structural interpretation, and batch analysis.
- Basic software features enable data investigation by showing mass differences between peaks, generating background subtracted spectra, merging related spectra, or creating contour plots
- Spectra from multiple samples can be viewed simultaneously in a single window such as with 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 IDA viewer presents data in a convenient graphic and tabular view with handy tools to filter the data based on criteria such as quality, mass defect, and isotopic pattern
- An XIC Manager enables fast generation of extracted ion chromatograms for 1000's of compounds in seconds
- Specialized tools such as Formula Finder and Structure Elucidation enable detailed investigation and characterization at the molecular level
- Functionality for working with MS/MSALL data (precursors of all products) enables visualization of the entire fragmentation space from this unique scan type in a single plot, enabling instant comprehension of common fragments and neutral losses
- The Protein Quantitation MicroApp enables the selection of peptides and proteins, extraction of MS peak areas, and exporting data to MarkerView™ Software to allow quantitation of all confident proteins, just a subset of proteins, or only specific peptides of interest
Status: Available 
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 recalibration tools based on found common background ions or experimentally determined fragment masses ensure highest accuracy mass reporting. Figure 1: The Formula Finder Tool
Structure Elucidation PeakView® software contains tools to link 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: Example of Structure of Buspirone 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 table for defining a list of masses or formula to generate XICs, as well as the ability to review the results of the XIC 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 used to sort. In addition, the results can be filtered to only display specific data or search 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 exporting of data to MarkerView Software. Once in MarkerView Software, the data can be analyzed using statistical analysis tools to determine groups of similar 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.
For Research Use Only. Not for use in diagnostic procedures.
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