Companies
Bioinformatics Solutions Inc.
Software
ProteoformX - User-friendly Software ...

ProteoformX - User-friendly Software Platform

Proteins are essential for carrying out the functions necessary for life. More precisely, proteoforms which are generated from genetic variation, alternative splicing, and post-translational modifications (PTMs) define function (or dysfunction) within an organism and drive cellular functions at the molecular level. ProteoformX^™ is a powerful, user-friendly software platform designed to make intact and top-down mass spectrometry accessible and actionable. It combines rapid intact mass profiling to globally assess detectable proteoform diversity with in-depth top-down analysis to resolve full protein sequences, map modifications, and enable quantification.

High precision mass deconvolution

Feature-based mass deconvolution identifies proteoform masses with high sensitivity and specificity, for isotopically resolved or unresolved data, across a wide range of sample types.

Comprehensive sample annotation with modifications and ADC drug payload

Intact mass workflow delivers accurate annotation for complex and sub-unit proteoforms, even for heterogeneous samples with modifications and ADC drug payload.

Glycosylation profile at proteoform level

Intact deconvolution accurately detects the glycosylated proteoforms of an antibody mixture.

Antibody heavy chain and light chain paring

Intact annotation determines antibody heavy and light chain pairings, enabling characterisation of all antibody forms, including asymmetric antibodies and mixture.

Comprehensive result view

ProteoformX^™ provides a comprehensive results including interactive spectrum views with annotated peaks for transparent interpretation, along with support features in mass deconvolution tables that can be directly used to guide targeted top-down MS/MS experiment.

Flexible Definition and Visualisation of Proteoform Variants

The Proteoform Manager in ProteoformX^™ provides an intuitive interface for defining intra- and inter-chain linkages, cleavage sites, site-specific PTMs, and glycosylation events. These capabilities support comprehensive modelling of complex proteoforms relevant to biopharmaceutical analysis.

Top-down MS enables in-depth characterisation of proteoforms, including precise PTM localisation. However, challenges such as data complexity and limited sequence coverage can limit throughput. In ProteoformX^™ , the unparalleled user interface helps user to manual check result from raw data to identification. Diverse fragmentation methods (CID, HCD, ETD, ETHCD, UVPD) were supported.

Trace every proteoform with hierarchical insight

In the Protein tab, the protein coverage shows proteoforms mapped to the protein sequence. Grey bars indicate regions where a mass tag is associated with the sequence, representing a mass shift and possible modification. However, these regions lack fragment ions for site-specific localisation of the mass tag.

In the Proteoform tab, the sequence coverage is defined by the percentage of the amino acid sequence supported by top-down fragment ions. Modifications or mass shifts with respect to the mass of the amino acid sequence are shown.

A deeper dive into the Proteoform tab shows how each ID is supported by high-quality PrSMs (deconvoluted MS2 spectra), fragment ion mass table and interactive sequence fragmentation maps.

The Spectrum tab in ProteoformX^™ overlays theoretical precursor peaks and fragment ions directly onto the MS1 and MS2 scans—so you can visualise isotopic envelopes, assess isolation windows, and see exactly which ions contributed to the deconvolution or even can get the chimera spectrum information. Colour-coded annotations make it easy to distinguish ion types and unmatched fragments, giving you unmatched transparency and confidence in your results.