What types of input files does ProteoAnalyst support?

ProteoAnalyst
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In addition to generic tab-delimited text file (.txt) or a comma-separated value file (.csv) containing protein IDs and intensity values, ProteoAnalyst currently accepts outputs from four common proteomics processing pipelines including:

  • MaxQuant: protein-level analysis using proteinGroups.txt (LFQ/iBAQ/Intensity) or peptide-level analysis using peptides.txt .
  • FragPipe: protein-level analysis using combined_protein.tsv (MaxLFQ/Intensity) or peptide-level processing using combined_peptide.tsv or combined_ion.tsv .
  • DIA-NN: protein-level analysis using pg_matrix.tsv (MaxLFQ/Quantities) or precursor-level processing using report.tsv
  • Spectronaut: standard protein or peptide report files.
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