Skyline

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

1 shared topic • 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,

1 shared topic • 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

1 shared topic • 1 shared operation

DIA-NN (Data-Independent Acquisition by Neural Networks) is a universal software suite for DIA proteomics data analysis. Processes raw mass spectrometry files (.mzML, .raw, .d, .wiff) using neural net

1 shared topic • 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

1 shared topic • 1 shared operation