synapter

synapter reanalyzes label-free proteomics data acquired on Synapt G2 q-TWIMS-TOF instruments using traveling wave ion mobility separation (TWIMS) to improve peptide and protein identification and quantitation.

Key Features:

• TWIMS-enabled identification accuracy: Uses the additional precursor separation dimension from TWIMS to improve assignment of fragment ions to their precursors in data-independent acquisition (DIA) datasets.
• Increased proteome coverage: Supports fragmentation post-TWIMS to achieve up to 60% higher proteome coverage compared to traditional methods.
• Improved quantitation of low-intensity ions: Leverages increased peak capacity from TWIMS to enable more accurate and precise quantitation of lower intensity precursor ions.
• Signal loss mitigation: Deconvolutes attenuation caused by ion scattering and detector saturation (IMS concentration effect) through analysis of peptide isotopic envelopes to reduce impact on quantitation.
• Optimization strategies for IMS/MS: Provides insights into the origin and extent of TWIMS-associated signal loss and suggests experimental strategies to minimize these effects, adaptable to other IMS/MS platforms.

Scientific Applications:

• Accurate peptide and protein identification: Improves fragment-to-precursor assignment in DIA data acquired on q-TWIMS-TOF instruments.
• Expanded proteome profiling: Enables deeper proteome coverage for complex biological samples via fragmentation after TWIMS.
• Quantitation of low-abundance species: Enhances detection and quantitation of low-intensity peptides and proteins by increasing separation peak capacity.

Methodology:

Integrates data from one or several runs processed with ion mobility separation and combines these runs with other quantitation files; deconvolutes signal loss by analysis of peptide isotopic envelopes and employs algorithms to handle TWIMS-induced complexities.