Thermo Scientific™

PepFinder™ Software

Related applications:

Industrial Mass Spectrometry

For biotherapeutic proteins to be effective, they must be produced in biologically active forms with proper folding and post-translation modifications (PTMs). Thermo Scientific™ PepFinder™ software provides accurate identification, in-depth characterization, and relative quantitation of biotherapeutic and other proteins from mass spectrometric data. It provides an automated workflows for glycopeptide identification, disulfide bond mapping, and quantification of PTMs. PepFinder software automates previously time-consuming manual processes, processing complex data and integrating the results into concise, informative reports.
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Easier Experimental Setup
PepFinder software makes it easy to define the target protein sequence, select a proteolytic digest enzyme, and assign known and potential post-translational modifications to search. Protein sequences can be imported from FASTA and text files, or sequences can be pasted into a text box.

Support for Custom Modifications
Beyond its extensive library of common modifications, PepFinder software supports the creation of the user-created custom modifications essential to antibody drug conjugate (ADC) studies.
Support for All Modes of Fragmentation
PepFinder software takes full advantage of mass spectrometer capabilities, supporting electron transfer dissociation (ETD) and higher-energy collisional dissociation (HCD) as well as collision-induced dissociation (CID).
Fast, Accurate Component Detection
PepFinder software provides fast, automated component detection - detection of peptide mass, retention time, and abundance. Multiple, unique component detection algorithms are tailored to different experiment and instrument types for faster, more accurate analyses.
Identification of Unspecified Modifications and Substitutions
Error-tolerant search enables identification of unspecified modifications and amino acid substitutions. A fragmentation map can easily be generated for confirmation.
Disulfide Bond Linkage Determination
PepFinder software automates the determination of disulfide bond linkages, a task extremely difficult to do manually. Mapping of disulfide bond linkages is achieved by processing non-reduced data files. No previous knowledge of the linkage sites is required, so novel linkages and potential disulfide bond scrambling can be identified and confirmed by MS/MS. Non-reduced and reduced data set can be compared for additional confidence.
Comparison Across Samples
Comparison of multiple samples provides extra confidence in disulfide mapping experiments by facilitating comparison of non-reduced and reduced conditions.
Faster Processing
The PepFinder software is 64 bit enabled, eliminating memory limitations and allowing it to take advantage of the latest computer technology for faster sample processing.
Automated Report Generation
PepFinder software generates comprehensive, site-specific modification summaries and sequence coverage maps for targeted proteins, eliminating difficult, tedious manual summarization.

Specifications, terms, and pricing are subject to change. Not all products are available in all countries. Please consult your local sales representative for details.