Thermo Scientific™ PepFinder™ software is a powerful new tool for automatic identification and relative quantification of biotherapeutic proteins with in depth characterization of Post-Translational Modifications (PTMs) of mass spectrometric data obtained from LC-MS experiments. Using the industry-leading, high-resolution, accurate-mass Thermo Scientific™ Orbitrap™  technology with exclusive PepFinder software, the most accurate and confident PTM profiles and identifications can be achieved more quickly than ever before.

Targeted protein/peptide quantitation is an integral step in proteomics research. Its application includes biomarker discovery, differential proteomics, signaling pathway analysis, and PTM expression studies and has traditionally been implemented exclusively using triple quadrupole mass spectrometers.

Thermo Scientific™ Pinpoint™ software is illustrated in the following workflows.

• Discovery to targeted using iSRM
• Hypothesis to targeted analysis
• Absolute Quantification

Even after preliminary identification and validation, scientists face the critical, time-consuming task of interpreting their proteomics data - extracting meaningful biological information from multiple, complex data sets. Thermo Scientific™ ProteinCenter software is a web-based data interpretation tool that enables scientists.

ProteinCenter software is illustrated in the following workflows.

• TGO annotation analysis
• Pathway based protein selection
• Biological interpretation of proteins

Automated, label-free, semi-quantitative analysis of proteins, peptides, and metabolites based on comparisons of LC/MS and GC/MS data Discovery of protein and metabolite biomarkers is an important step in understanding metabolic pathways and disease mechanisms, and in identifying potential drug and diagnostic targets.

Thermo Scientific™ SIEVE™ software is illustrated in the following workflows.

• Protein Biomaker Discovery
• Small Molecule Maker Discovery
• Two-Pass Refined Discovery

User application can listen to scan data streams, monitor and refine instrument parameters or deploy user defined scans at runtime. An event-driven architecture provides the capability to synchronize application workflows and react instantly on upcoming scenarios. The access and analysis of the incoming scan.

Thermo Scientific™ ProSightPC software, the first stand-alone software for analyzing top-down proteomics data, has been enhanced to add support for middle-down and bottom-up experiments, making it an all-around tool for identification and characterization of both intact proteins and peptides.

ProSightPC software is illustrated in the following workflows.

• Top Down protein MS/MS ID
• Elucidation of unknown PTMs
• Protein database curation

Deep data mining by combining multiple search engines and information from multiple dissociation techniques. Utilize advanced tools for database search results validation and statistically rigorous estimation of false discovery rates. Percolator for maximizing the number of true positive Peptide Spectrum matches.

Thermo Scientific™ Proteome Discoverer™ software is illustrated in the following workflows.

• Iterative search strategies
• Multi-search engine comparison
• iTRAQ/TMT quantification