QuantMS Input Files

QuantMS Input Files#

See the documentation for an overview: docs.quantms.org

Sample Data Relationship Format (SDRF) file#

  • describes the relationship between the biological samples and the (raw) data files from the mass spectrometer

Example from PXD04621: PXD040621.sdrf.tsv

Fasta File#

  • defines the search space: only these protein sequences will be considered for the spectrum database search

Example from PXD04621: merged_ecoli_with_contaminants.fasta

Spectrum Files#

  • contains the spectra which are compared to the protein sequences in the fasta file to identify the proteins (actually peptides) in the sample

Example from PXD04621, see download instructions on the page ‘QuantMS Hands-On for PXD04621’

QuantMS Parameters file#

  • defines the parameters for the analysis, e.g. the search engine to use, the quantification method, the database to use, etc.

Example from PXD04621: PXD040621_w_contaminants-params.yaml

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