Key Features

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Top-down Proteome Search

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 users to manually check the result from raw data to identification. Diverse fragmentation methods such as CID, HCD, ETD, ETHCD, and UVPD are supported.

In-depth top-down proteome identification with open search

Enabling OpenPTM Search increases proteoform identification by allowing for unexpected modifications and truncated forms. In the example below, only two C-terminal proteoforms of the B8ZZQ6 protein were identified without OpenPTM Search, while eight were detected when it was enabled. One of these additional proteoforms featured a –89.03 Da mass shift, consistent with methionine loss and N-terminal acetylation—an established but often overlooked modification. By broadening the search space to include mass shifts and non-canonical termini, OpenPTM Search enables more comprehensive and accurate proteoform profiling.

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Intact Mass Analysis

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New Peak Detection

New Peak Detection detects emerging peaks and tracks variation trends in biopharmaceutical metabolites, product‑related impurities, and molecular changes. Essential for characterizing complex biopharmaceutical molecules by mass spectrometry, this feature also supports linear, branched, and cyclic peptides, including sequences containing unnatural amino acids and nucleotides, with added manual validation to support pharmaceutical workflows. 

Characterization of peptides with unnatural amino acids and nucleotides

Peptide biotherapeutics commonly have unnatural amino acids (UAAs) and unnatural nucleotides (UNs). However, common mass spectrometry data analysis tools were built with limitations to search only the canonical amino acids. In this module users can define UAAs/UNs, where New Peak Detection will use both MS1 and MS2 data to enable confident identification and quantification, monitoring trends of molecular changes. Improving the accurate analysis and characterization of complex peptide biotherapeutics. 

Characterization of linear, branched, and cyclic peptides

Many biotherapeutics are no longer simple linear molecules, they can include branched or cyclic structures, requiring specialized annotations and analysis. New Peak Detection supports linear, branched, and cyclic structures providing specialized MS2 annotations for branching, ring openings, and cleaved cyclic peptide fragmentation (the yellow dotted line indicates the ring opening at disulfide bond; the black vertical bar is a cleavage site). Additionally, to help users verify the accuracy of their input, a mass validation tool is provided, which calculates the theoretical masses generated at different cleavage positions. This allows for monitoring variation trends of complex molecules with high sensitivity. Finally, map impurities against a background protein FASTA or search for novel peptides using de novo.

Manual editing of feature detection

Automated feature detection may miss certain features due to factors such as low concentrations of degradation products, peak shape inference, or matrix effects. The Feature Editor function is designed to address this challenge by allowing users to manually and accurately select and define incorrectly detected or previously unidentified features in the target chromatogram. Use the feature editor button to access the manual feature detection interface.

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Peptide Mapping

Peptide Mapping is one of the latest newly featured workflows in ProteoformX. It enables the characterisation of proteoforms from enzymatically digested samples. That includes mapping of peptide sequences to various proteoforms, identification of post-translational modifications (PTMs) and sequence variants using peptide-level information.

Bottom-up MS data can now be utilized to characterise the complete proteoform landscape of target proteins with the newly incorporated PTM profiling functions. Featuring the PEAKS PTM and Open PTM search algorithms, Peptide Mapping now enables identification and quantification of not only known and common modifications, but also uncommon and unknown modifications. Together with the use of Sequence Variants function for identification of mutations, this workflow enables users to acquire a complete overview of possible proteoforms that provides functional insights.

Aside from the enhanced qualitative features, users can also investigate quantitative variations between samples. By selecting Representative Peptides in the Feature or Peptide tabs, users can manually inspect changes of peptide abundance across samples to inform functional outcomes or batch differences.

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Proteoform Manager

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