Thermo Scientific Pinpoint Software - Thermo Fisher :: Orbitrap
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Part of Thermo Fisher Scientific mass spectrometry Accelerating targeted protein quantitation in biological research Thermo Scientific Pinpoint Software
Transcript of Thermo Scientific Pinpoint Software - Thermo Fisher :: Orbitrap
Part of Thermo Fisher Scientific
m a s s s p e c t r o m e t r y
Accelerating targeted protein quantitation in biological research
Thermo Scientific Pinpoint Software
Thermo Scientific Pinpoint Softw
are
Targeted protein/peptide quantitation is an invaluable tool for proteomics research.
Applications include biomarker discovery, differential proteomics, signaling pathway
analysis, and PTM expression studies. Targeted analysis extends detection limits,
provides high-confidence verification, and dramatically reduces analysis time required
to discern putative protein/peptide targets. Targeted quantitation is being employed
earlier and in more areas of proteomics research. This often results in an increased
number of protein and peptide candidates being monitored, putting greater
demands on software tools.
Thermo Scientific Pinpoint software provides unique strategies to leverage discovery
data from local and global repositories to expedite method building and data processing.
Its advanced tools for identifying, characterizing, and quantifying biological samples
provide a complete start-to-finish solution for biomarker identification and verification.
PinpointTM software can process MSn and high-resolution/accurate-mass (HR/AM)
data as well as traditional selected reaction monitoring (SRM) transition data. This makes
it compatible with ion trap and hybrid ion trap / OrbitrapTM mass spectrometers in addition
to the triple quadrupoles more commonly used for targeted quantitation.
Pinpoint Software – Facilitating Protein Quantitation to Further Proteomics Research
Pinpoint software facilitates many tasks within a quantitative proteomics workflow
Simplifying Quantitation Through Powerful Tools
Powerful, integrated tools in the Pinpoint software simplify virtually every step of a targeted quantitation workflow. The software:
• Integrates discovery data and in silico predictions to automatically build large, robust lists of targeted peptides for more-intelligent data acquisition and extraction.
• Employs a unique peptide screening tool for deeper interrogation of full-scan, high-resolution/accurate-mass (HR/AM) MS data, facilitating identification of missed cleavages, combinations of post-translational modifications (PTMs), and truncated proteins.
• Enables automated building of timed acquisition methods based on calculated hydrophobicity factors, previously measured library data, or synthetic peptide-based LC calibrators for increased target interrogation without sacrificing precision.
• Provides automated data processing support, improving all levels of quantitation – relative,
absolute, single-point, time-course studies, and quantitation curve generation for normal and reverse curves.
• Combines quantitative, hierarchical results tables with interactive graphical representation of protein, peptide, precursor, and product ion information for simplified data review.
• Facilitates refinement of targeted discovery lists for Orbitrap analzyer-based hybrid mass spectrometers and transition lists for triple quadrupole SRM assays.
In a single package, Pinpoint software allows you to proceed from creating protein/peptide-based target lists all the way to processing data
Step 1. Define the protein/peptide targets
Target protein sequences are defined by the user. They can be manually entered or uploaded from database search results. Pinpoint software can link to global spectral data repositories and integrate discovery experiments from multiple laboratories, expanding the amount of background proteomic information available for building experimental methods.
Step 3. Create acquisition methods for simple or complex assays
Pinpoint software can be used to efficiently generate both scheduled and non-scheduled methods. Its unique retention time prediction functions help automate the development of highly multiplexed experiments that can reduce the need for multiple injections.
Step 2. Determine m/z values for data acquisition or processing
Target m/z lists are generated automatically based on user-defined peptide selection and data acquisition/processing strategies. Methods are easily generated for HR/AM, lower-resolution MSn, or SRM methods.
Streamlining the Experimental Methodology – Stepwise Progression from Hypothesis to Results
Step 4. Organize and process data
Targeted protein/peptide quantification workflows can take numerous forms. Pinpoint software has the flexibility to organize data, set different threshold and integration parameters, and group large data sets acquired over time.
Step 5. Review data and verify peptide candidates
Pinpoint software features a common data analysis interface for all MS levels, from HR/AM data to simultaneous HCD activation of all precursors (all-ion activation) to MSn to SRM transition information. The software provides complete tabular information as well as interactive graphical representations for easy review and verification. Many different strategies can be used to evaluate data and select appropriate peptide candidates.
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Step 6. Refine the method
Pinpoint software provides many strategies for extracting ideal peptide candidates from one experiment and applying them to the next experiment. Information such as retention time windows, precursor charge states, and product ions can be used to create libraries. Additional verification tools such as peptide-based hydrophobicity factors can relate measured retention times to predicted retention times. Refined methods can be stored as libraries or transferred back into the Main Workbook for a more accurate data acquisition/processing method.
Managing Information from Targeted Protein/Peptide QuantitationTargeted quantitation presents many challenges as protein/peptide targets from discovery experiments are transitioned to routine protein quantitation assays. Pinpoint software provides unmatched tools for all stages of targeted quantitation workflows including identifying key peptide sequences and modifications, determining optimum m/z values for precursor and product ions, and performing all types of data analysis. Data support includes single-point quantitation and detection, calibration curves, time-course analysis, and large cohort analysis. In addition, Pinpoint software provides unmatched scalability and cross-platform portability.
