Pinpoint™ Software

Transition from early-stage biomarker discovery to larger-scale, quantitative verification of putative biomarkers and general quantitative proteomics with the Thermo Scientific™ Pinpoint Software.

Pinpoint software simplifies the creation of targeted quantitative assays. It allows researchers to leverage previously acquired data from discovery experiments. Pinpoint software largely automates the development of preliminary methods. It enables acquisition and analysis of preliminary data, which is in turn used to optimize the method.

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Product Description

Thermo Scientific Pinpoint was created specifically to simplify the creation of iSRM assays. Using data from discovery experiments, Pinpoint software largely automates the preliminary selection of SRM transitions to be monitored. It predicts proteotypic peptides, determines the best SRM transitions, and builds the TSQ instrument method.

The iSRM workflow development process is iterative. The preliminary method is used to acquire data, which is in turn used to refine the method. Pinpoint software also provides tools for evaluating this preliminary data. The target peptides that show the best responses are retained while target peptides that do not show good responses are removed from the final iSRM method. This ensures that the limited, fixed cycle time is used to analyze only peptides that provide high-quality results.

  • Easy import and processing of panels of targeted proteins/peptides selected from discovery experiments
  • Automated searching of user-created and public (e.g. Peptide Atlas) MS/MS spectral libraries, or in-silico prediction of target peptides for hypothesis-driven experiments
  • Automated selection of the most abundant precursor and product ions, with highly accurate, automated determination of optimal collision energies for SRM transitions
  • Flexible method design that can integrate high-resolution precursor selection, timed acquisition, and full MS/MS scans (QED) into SRM assays
  • Spectral matching capabilities between experimental and library data provides unique correlation analysis with probability scoring for targeted peptide verification with high confidence.
  • Customizable reports that can integrate discovery results with relative and absolute quantitation results
  • Easy result export for method refinement for subsequent qualitative and quantitative experiments

Compatible with:

  • Proteome Discoverer software
  • SIEVE software
  • TSQ family of triple quadrupole mass spectrometers
  • HeavyPeptide AQUA custom heavy peptides
  • SILAC reagents and kits
  • Tandem Mass Tags (TMT)


Leveraging discovery data

The ability to leverage data from qualitative discovery experiments can vastly simplify development of targeted proteomics methods and speed verification of putative biomarkers.

Targeted assays

High-resolution, accurate-mass data can enhance quantification of peptides, particularly in complex samples.  Pinpoint software facilitates the development, operation, and analysis of these quantitative assays.

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Catalog #
For Use With
Proteome Discoverer Software; SIEVE software; TSQ Family of Triple Quadrupole Mass Spectrometers; HeavyPeptide AQUa Custom Heavy Peptides; SILAC Reagents and kits; Tandem Mass Tags (TMT)

Full specifications
For Use With Proteome Discoverer Software; SIEVE software; TSQ Family of Triple Quadrupole Mass Spectrometers; HeavyPeptide AQUa Custom Heavy Peptides; SILAC Reagents and kits; Tandem Mass Tags (TMT)
Type Software
Description Pinpoint Software

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