quantms

DIA-NN R package — R toolkit for post-processing DIA-NN proteomics search results. Provides report loading (diann_load), precursor/peptide/protein matrix generation with FDR filtering (diann_matrix),

2 shared topics • 2 shared operations

MSnbase routing skill for R/Bioconductor mass spectrometry data handling, preprocessing, and quantification. Use this skill when users mention MSnbase, MSnExp, OnDiskMSnExp, MSnSet, LC-MS/MS preproces

2 shared topics • 2 shared operations

Philosopher — fast, scalable Go toolkit for shotgun proteomics data analysis. Provides database downloading, peptide validation (PeptideProphet), protein inference (ProteinProphet), PTM localization (

2 shared topics • 2 shared operations

Comet — open-source tandem mass spectrometry (MS/MS) sequence database search engine for peptide identification. Searches MS/MS spectra against FASTA protein databases producing pepXML, mzIdentML, SQT

2 shared topics • 1 shared operation

Use when working with Crux — the University of Washington Noble Lab's open-source toolkit for bottom-up tandem mass spectrometry (MS/MS) proteomics analysis. Covers the full peptide identification pip

2 shared topics • 1 shared operation