File Loader

AlphaPeptLoader

class AlphaPeptLoader(file, intensity_column='[sample]_LFQ', index_column='Unnamed: 0', sep=',', **kwargs)

Loader for AlphaPept outputfiles https://github.com/MannLabs/alphapept

DIANNLoader

class DIANNLoader(file, intensity_column='[sample]', index_column='Protein.Group', sep='\t', **kwargs)

Loader for DIA-NN output files https://github.com/vdemichev/DiaNN

FragPipeLoader

class FragPipeLoader(file, intensity_column='[sample] MaxLFQ Intensity ', index_column='Protein', gene_names_column='Gene Names', confidence_column='Protein Probability', sep='\t', **kwargs)

Loader for FragPipe-Philosopheroutputfiles https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#combined_proteintsv

MaxQuantLoader

class MaxQuantLoader(file, intensity_column='LFQ intensity [sample]', index_column='Protein IDs', gene_names_column='Gene names', filter_columns=['Only identified by site', 'Reverse', 'Potential contaminant'], confidence_column='Q-value', evidence_file=None, sep='\t', **kwargs)

Loader for MaxQuant outputfiles

SpectronautLoader

class SpectronautLoader(file, intensity_column='PG.Quantity', index_column='PG.ProteinGroups', sample_column='R.FileName', gene_names_column='PG.Genes', filter_qvalue=True, qvalue_cutoff=0.01, sep='\t')

Loader for Spectronaut outputfiles

mzTabLoader

class mzTabLoader(file, intensity_column: str = 'protein_abundance_[sample]', index_column: str = 'accession')