Tool Field Mappings¶
Reference for converter developers
This page is a reference for converter developers. For schema definitions, see the individual view pages: PSM, Feature, Protein Group.
This page documents how fields from different proteomics search engines and tools map to the corresponding QPX fields. Each section covers a specific QPX view and lists the source column name in each supported tool.
A dash (---) indicates that the tool does not provide a direct mapping for that field.
PSM Field Mappings¶
The PSM (Peptide Spectrum Match) view captures spectrum-level identification results. The table below shows how each QPX PSM field maps to columns in common proteomics tools.
| QPX Field | MaxQuant | DIA-NN | FragPipe | mzTab |
|---|---|---|---|---|
sequence |
Sequence | Stripped.Sequence | Peptide | sequence |
peptidoform |
Modified sequence | Modified.Sequence | Modified Peptide | opt_global_cv_MS:1000889_peptidoform_sequence |
charge |
Charge | Precursor.Charge | Charge | charge |
posterior_error_probability |
PEP | PEP | --- | opt_global_Posterior_Error_Probability_score |
is_decoy |
Reverse | --- | --- | opt_global_cv_MS:1002217_decoy_peptide |
calculated_mz |
--- | --- | Calculated M/Z | calc_mass_to_charge |
observed_mz |
m/z | --- | Observed M/Z | exp_mass_to_charge |
protein_accessions |
Proteins | Protein.Group | Protein | accession |
run_file_name |
Raw file | Run | Spectrum File | spectra_ref |
scan |
Scan number | --- | Scan | --- |
rt |
Retention time | RT | Retention | retention_time |
PEP direction
posterior_error_probability is the probability that the PSM is incorrect — lower values indicate higher confidence (lower is better). All major tools (Percolator, MaxQuant) export PEP directly as P(incorrect). FragPipe exports PeptideProphet Probability (P(correct)), so PEP must be computed as 1 - probability.
Feature Field Mappings¶
The Feature view captures quantified peptide features with intensity data. Features aggregate information across scans and are the primary view for DIA and label-free quantification workflows.
| QPX Field | MaxQuant | DIA-NN | FragPipe | mzTab |
|---|---|---|---|---|
sequence |
Sequence | Stripped.Sequence | Peptide | sequence |
peptidoform |
Modified sequence | Modified.Sequence | Modified Peptide | opt_global_cv_MS:1000889_peptidoform_sequence |
charge |
Charge | Precursor.Charge | --- | charge |
is_decoy |
Reverse | --- | --- | opt_global_cv_MS:1002217_decoy_peptide |
calculated_mz |
--- | --- | Calculated M/Z | calc_mass_to_charge |
observed_mz |
m/z | --- | --- | exp_mass_to_charge |
rt |
Retention time | RT | --- | retention_time |
rt_start |
--- | RT.Start | --- | --- |
rt_stop |
--- | RT.Stop | --- | --- |
predicted_rt |
--- | Predicted.RT | --- | --- |
intensities |
Intensity | Precursor.Quantity | Intensity | Intensity |
pg_accessions |
Proteins | Protein.Group | --- | accession |
anchor_protein |
--- | --- | --- | --- |
pg_positions |
--- | --- | --- | --- |
run_file_name |
Raw file | Run | --- | --- |
Protein Group Field Mappings¶
The Protein Group view captures protein-level quantification and inference results. The table below covers the three main supported tools; mzTab protein group mapping is handled through the PSM and Feature views.
| QPX Field | MaxQuant | DIA-NN | FragPipe |
|---|---|---|---|
pg_accessions |
Protein IDs | Protein.Group | Group + Indistinguishable Proteins |
pg_names |
Protein names | Protein.Names | --- |
gg_accessions |
Gene names | Genes | --- |
run_file_name |
combined | Run | --- |
peptide_counts |
Unique peptides | Unique.Stripped.Peptides | Unique Peptides |
feature_counts |
MS/MS count | Precursor.Quantity | Precursor Ions |
global_qvalue |
Q-value | Global.PG.Q.Value | --- |
intensities |
Intensity, LFQ intensity | PG.Quantity | --- |
additional_intensities |
LFQ intensity, iBAQ | PG.Normalised, PG.MaxLFQ | --- |
is_decoy |
Reverse | --- | --- |
contaminant |
Potential contaminant | --- | --- |
Tool version considerations
Column names may vary between tool versions. The mappings above reflect the commonly used versions at the time of writing:
- MaxQuant: v2.x (
evidence.txt,proteinGroups.txt) - DIA-NN: v1.8+ (
report.tsv,pg_matrix.tsv) - FragPipe: v20+ (combined output files)
- mzTab: v1.0 specification columns
Adding support for a new tool
To add a converter for a new tool, implement a mapping from the tool's output columns to the QPX fields listed in the tables above. See the PSM, Feature, and Protein Group schema pages for field type requirements and nullability constraints.