- Intelligent data acquisition for top-down proteomics (FLASHIda)
- Feature level label-free quantification algorithm for top-down proteomics (FLASHDeconvQ)
- SRM Quantitation and QC (SmartPeak 2)
- Protein-nucleic acid cross-linking (OpenNuXL)
- Efficient Bayesian protein inference (EPIFANY)
- Ultra-fast MS1/MS2 deconvolution for top-down proteomics: FLASHDeconv 2.0 beta+, finally with a GUI!
- Nucleic Acid Search Engine (NASE)
- Protein-Protein Cross-Linking (OpenPepXL)
- RNA-Protein Cross-Linking (RNPxl)
- Stable Isotope Probing (MetaProSIP)
DIAproteomics: Automated quantitative analysis of DIA proteomics mass spectrometry measurements
DIAproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independent (DIA) proteomics data.
The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral library. If specified internal retention time standards (irts) will be used to align library and DIA measurements into the same retention time space. FDR rescoring is applied using Pyprophet based on a competitive target-decoy approach on peakgroup or global peptide and protein level. Optionally EasyPQP can be used for library generation and DIAlignR for chromatogram alignment and quantification.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
The Nextflow Workflow is available at:
See also the detailed description of parameters and workflow output at: