Licensed

· top-down proteomics analysis
· modification identification
· cleavage/truncation identification
· label-free quantitation
· antibody identification

· targeted top-down analysis
· intact mass profiling & quant
· biologics & protein-ligand screening
· proteoform database search
· protein complex analysis

Free

· fragment matching
· fragment map visualization

· Direct Mass Technology™ MS data
processing, visualization, and
analysis

· database management, curation,
and customization

· proteomics result visualization
and reporting

top-down proteomics analysis

Analyze top-down proteomics data using our powerful ProSight database search engine. ProSightPD can flexibly process a wide range of Thermo™ TDMS data— from single proteoform analysis to large, high-throughput top-down proteomics experiments— with speed and precision. A wide range of visualization tools (including TDValidator, ProSight Lite, and TDViewer) and annotation tools (including Database Manager and ProSight Annotator) enable comprehensive data review and analysis.

modification identification

Search modifications with confidence. By using annotated modifications from UniProt™ or custom XML files, ProSightPD assigns only modifications with empirical evidence for their existence. Unknown mass shifts can also be used to account for mass differences and to assign additional fragmentation ions. 

cleavage/truncation identification

Look for and identify endogenous cleavages, protein truncations, and clipping products. Cleavage sites can be determined on the N-terminus, C-terminus, or both termini.

label-free proteoform quantitation

Quantitate differences in proteoform abundances across label-free sample types using the Proteome Discoverer™ statistical engine. Sliding window deconvolution with kDecon and Xtract unlocks robust quantitation for proteoform masses, large and small.

antibody identification

Search large mass data such as antibody subunits and intact antibodies using the high mass capabilities of ProSightPD. The kDecon algorithm can determine masses from large proteoforms with unresolved charge state distributions, which can narrow the search range. Integration with ProSight Annotator allows custom sequences and modifications to be annotated and searched.

key applications

complex-down analysis

Unveil the full composition and stoichiometry of a protein complex using ProSight Native’s unique workflow to analyze each level of a complex-down mass spectrometry experiment:

1. Intact complex mass analysis

2. Subunit mass analysis

3. Subunit fragmentation analysis.

ProSight Native is currently the only software available that can perform all 3 analysis components.

protein complex composition determination 

Assess protein complex and subunit masses with mass deconvolution algorithms. ProSight Native integrates our flagship ProSight database search engine, allowing you to then elucidate subunit proteoform identities. The software automatically compiles the data to yield the full stoichiometry of subunits and even non-covalently-bound ligands associated with the complex. 

protein mass determination

Determine masses for isotopically-resolved and -unresolved proteins. ProSight Native combines kDecon and THRASH deconvolution for incredibly fast analysis of any size proteins.

proteoform database search

Search proteoform fragmentation data against candidate proteoforms using ProSight search. Candidates are composed of full length or truncated isoform sequences with site-specific post-translational modifications.

top-down mass spectrometry analysis

Perform targeted analysis of a single proteoform or multiple proteoforms. Our TDValidator tool lets you input proteoforms for a single fragment spectrum and match all of the theoretical fragment ions to the spectral data. You can also match precursor ions to precursor spectral data. Fragmentation matching can be performed on data from a wide range of fragmentation techniques, including CID, HCD, ETD, ECD, EThcD, ETciD, and UVPD.

proteoform characterization

Characterize proteoforms using fragmentation evidence. Analyze fragmentation spectra and corresponding matching ions to confidently localize proteoform modifications. TDValidator overlays matching ions from different proteoforms on the same spectra and uses a host of visualization tools and metrics to power in-depth study of proteoforms.

internal fragment ion discovery

Look for internal fragment ions formed during fragmentation processes. The ions can be visualized by color gradient heat map on the fragment map itself. Internal fragment ions can provide additional evidence for modification site localization, increasing confidence in assignments.

modification localization

Assess fragmentation coverage using fragmentation maps and related metrics. Fragmentation ion matches can be validated to confirm post-translational modification site assignments.

key applications

fragment matching

Match experimentally-derived fragment ion lists to theoretical fragment ions of a proteoform. A simple, straightforward interface allows modifications to be easily added to the proteoform. Confidence metrics such as a P-score and proteoform characterization score are calculated.

fragment map visualization

Visualize fragmentation matches using fragment flags to show N- and C- terminal fragmentation ions. Fragment flag colors correspond to the type of ion found. Post-translational modifications are color-coded for easy differentiation of modification type.

key applications

database management, curation, & customization

Create and curate UniProt™-formatted XML files using ProSight Annotator’s intuitive user interface, and customize the content of databases you create and search against. Protein sequences can be easily added, removed, or edited with post-translational modifications and other features of interest. The newly annotated XML files can then be used as databases in our ProSight tools. Begin by importing FASTA or UniProt™-formatted XML files.

key applications

proteomics result visualization and reporting

Display protein and proteoform results from a .tdReport. TDViewer allows you to filter results by false discovery rate (FDR) and specific input files. You can also visualize spectra fragmentation maps and Venn diagrams of search results across multiple samples.