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
`sequence`	Sequence	Stripped.Sequence	Peptide
`peptidoform`	Modified sequence	Modified.Sequence	Modified Peptide
`charge`	Charge	Precursor.Charge	Charge
`posterior_error_probability`	PEP	PEP	---
`is_decoy`	Reverse	---	---
`calculated_mz`	---	---	Calculated M/Z
`observed_mz`	m/z	---	Observed M/Z
`protein_accessions`	Proteins	Protein.Group	Protein
`run_file_name`	Raw file	Run	Spectrum File
`scan`	Scan number	---	Scan
`rt`	Retention time	RT	Retention

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	QuantMS MSstats
`sequence`	Sequence	Stripped.Sequence	Peptide	PeptideSequence (unmodified)
`peptidoform`	Modified sequence	Modified.Sequence	Modified Peptide	PeptideSequence (ProForma-normalized)
`charge`	Charge	Precursor.Charge	---	Charge / PrecursorCharge
`is_decoy`	Reverse	---	---	ProteinName prefix
`calculated_mz`	---	---	Calculated M/Z	---
`observed_mz`	m/z	---	---	---
`rt`	Retention time	RT	---	RetentionTime
`rt_start`	---	RT.Start	---	---
`rt_stop`	---	RT.Stop	---	---
`predicted_rt`	---	Predicted.RT	---	---
`intensities`	Intensity	Precursor.Quantity	Intensity	Intensity + Channel
`pg_accessions`	Proteins	Protein.Group	---	ProteinName
`anchor_protein`	---	---	---	First ProteinName accession
`pg_positions`	---	---	---	---
`run_file_name`	Raw file	Run	---	Reference / Run resolved through SDRF

Protein Group Field Mappings¶

The Protein Group view captures protein-level quantification and inference results. The table below covers the three main supported tools.

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)

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.