Analysis of single-cell proteomics data


This section organizes computational pipelines for the analysis of single-cell proteomics data. These pipelines can be used with data generated from various methods for single-cell proteomics.


SCoPE2 pipeline

The pipeline was developed to process the SCoPE2 data from Spech et al., 2019, but with small modifications it has been used with plexDIA and pSCoPE data as well.


Increasing confident peptide identifications

DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches.


Visualizing LC-MS/MS data

DO-MS is an an interactive open source platform for their interactive visualization and analysis of LC-MS/MS data: Data-driven Optimization of MS (DO-MS)