DIA-NN (diann-nextflow)

FlashLFQ — ultrafast label-free quantification for mass spectrometry proteomics. Quantifies peptide and protein abundances from MS/MS identifications using peak detection on raw/mzML spectra. Supports

2 shared topics • 2 shared operations

MSstats — Bioconductor R package for statistical analysis of quantitative mass spectrometry-based proteomics experiments. Supports label-free DDA, TMT, iTRAQ, SRM/MRM, and DIA workflows. Provides prep

2 shared topics • 2 shared operations

AlphaPept — Python-based, open-source proteomics pipeline for DDA mass spectrometry data analysis. Provides feature detection, peptide identification via database search, deep learning-based scoring,

2 shared topics • 1 shared operation

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

MaxQuant — quantitative proteomics platform for analyzing large-scale mass spectrometry data. Integrates the Andromeda search engine for peptide identification, supports label-free quantification (LFQ

2 shared topics • 1 shared operation