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Variant-Proteome-DB-Generator
A python command line based script for extraction of annotated variants from VCF file, generating variant proteome database and to check the uniqueness of variant proteins from the database search.PTM-Summarizer
Summarize post-translationally modified amino acid sites, peptides and proteins for Proteome Discoverer outputPTM-Site-Validator
Validation of modified amino acid sites in peptide sequences by identifying immonium ions in the raw spectra (.mgf format)MGF-file-splitter
Extract raw file specific spectra from an unassigned spectra file (.mgf) from Proteome Discoverer and generate new .mgf files specific to raw filesSpecAngle
Calculate Normalized Spectral Contrast Angle Score for Peptide Spectrum Matches (PSMs) using Prosit predicted peptide libraryMS-noise-eraser
DIA-SpecLib_Result_Summarizer
Extract the identified peptides and proteins from spectral library search of DIA proteomic data in SkylineSpecLib_Feature_Extractor
Extracts the features of peptide spectral library for better understanding and its efficient usage in DIA database searchPepAnnotate
Generate annotated Peptide Spectrum Matches (PSMs) from proteomic database search resultVarClassFDR
Calculate class FDR for variant peptides identified from Proteome Discoverer resultsGeneral_Scripts-Python
Identification, Counting the number of rows and Deleting of files based on suffix, prefix or other search terms in multiple directoriesR_Scripts
Routinely used R scripts in statistical analysis of proteomic experiment results with figure and plot generationUniformRT
LC-MS/MS derived peptide retention time deviation calculator across replicates for DDA and DIA derived result files.Proteogenomic-Pipeline
Python packages for easy execution of proteogenomic workflowPython-Scripts
Scripts used for proteomic data formatting and extractionBlib2OpenSwath
A Python script to convert the spectral library in BLIB format (.blib) from either Skyline or BiblioSpec to readable library format (OpenSwath or Spectronaut libraries)Uniqpepextractor
Tryptic peptides unique to a protein/species from a list of multiple proteins/species fasta files can be extracted.Love Open Source and this site? Check out how you can help us