Output Data

Calibration Data

The Calibration class outputs calibrated mzML files, which are based on the original mzML files, but with the m/z values corrected. The output files are named according to the original mzML file names, with the suffix “_calibrated” added. For example, if the original mzML file is named “sample.mzML”, the calibrated file will be named “sample_calibrated.mzML”. The calibrated mzML files are saved in the same directory as the original mzML files unless otherwise specified. This will be deprecated when the calibration is implemented in the InstaNovo pipeline.

Quantification Data

The INQuant class can output a variety of data files, based on user specifications. Default output files are the PSM table, the peptide table and if protein alignment is computed, the protein table. Other files, which can be written are the individual quantification files for each mzML file and the ungrouped protein table, which does not include protein inference.

Columns in the output files are as follows:

PSM table

Column Name	Description
sequence	Peptide sequence identified
seq_modifications	Sequence including the modifications on specific residues in the sequence
modifications	List of modifications present in the peptide
principal_protein*	The principal protein which the peptide aligns to
protein_matches*	Number of protein entries matching this peptide
no_protein_matches*	Number of unique matches to proteins
no_protein_groups*	Number of protein groups the peptide is part of
no_psms	Number of peptide-spectrum matches (PSMs) combined to this PSM
conf	Confidence score or level of identification
abundance	Quantitative measure of peptide abundance
charge	Charge state of the peptide ion
mz	Mass-to-charge ratio of the peptide ion
calc_mass	Theoretical calculated mass of the peptide
meas_mass	Measured mass from mass spectrometry
rt	Retention time during chromatography
id_scan	Identification scan number where the peptide was identified by InstaNovo
file_id	Identifier for the mzML file containing the scan
exp_file	mzML file name

*only if protein alignment is computed

Peptide table

Column Name	Description
sequence	Peptide sequence identified
seq_environment*	Environment of the peptide in the protein sequence
seq_modifications	Sequence including the modifications on specific residues in the sequence
terminal*	Terminal location, if any
principal_protein*	The principal protein which the peptide aligns to
principal_protein_start*	Start position of the peptide in the principal protein
principal_protein_end*	End position of the peptide in the principal protein
protein_matches*	Number of protein entries matching this peptide
protein_locs*	Locations of the peptide in the matched proteins
no_protein_matches*	Number of unique matches to proteins
no_protein_groups*	Number of protein groups the peptide is part of
no_psms	Number of peptide-spectrum matches (PSMs) combined to this peptide
conf	Confidence score or level of identification
meas_mass	Measured mass from mass spectrometry
abundance_[experiment_id]	Quantificaton values for each experiment (multiple columns)
abundance_[experiment_id]_normalized	Normalized quantification values for each experiment (multiple columns) based on the method specified by the user

*only if protein alignment is computed

Protein table

Column Name	Description
principal_protein	The principal protein which the peptide aligns to
description	Description of the protein
coverage_pct	Percentage of the protein sequence covered by identified peptides
protein_length	Length of the protein sequence
protein_group	Proteins in the group
no_protein_groups	Number of protein groups the protein is part of
peptide_seqs	List of peptide sequences aligned to this protein
no_peptides	Number of peptides aligned to this protein
no_unique_peptides_protein	Number of unique peptides aligned to this protein, not shared with other proteins in the group
no_unique_peptides_group	Number of unique peptides aligned to this protein group
no_psms	Number of peptide-spectrum matches (PSMs) combined to this PSM
abundance_[experiment_id]	Quantificaton values for each experiment (multiple columns) for the top N peptides aligning to this protein (N specified by the user)
abundance_[experiment_id]_normalized	Normalized quantification values for each experiment (multiple columns) based on the method specified by the user for the top N peptides aligning to this protein (N specified by the user)