SynapSpec writes the final analysis results to the selected output directory. The output file extension depends on the selected format: .csv, .parquet, or .tsv. The examples below use .csv, but the same file names are also available with .parquet or .tsv when those formats are selected.

For multi-run analyses, Match Between Runs (MBR) is enabled by default unless it is disabled in the settings. When MBR is enabled, the files below contain the final MBR-refined results and keep the standard names shown here. Intermediate search outputs and the temporary MBR spectral library are not exported as user-facing result files.

Standard Output Files

File	Description
precursors.<format>	Final precursor-level report with identification, protein annotation, q-values, and quantities.
fragments.<format>	Fragment ion-level report linked to the precursor report by precursor_index.
peptide.matrix.<format>	Peptide-level quantity matrix across runs.
precursor.matrix.<format>	Precursor-level quantity matrix across runs.
pg.matrix.<format>	Protein group-level quantity matrix across runs.
qc_report.pdf	PDF report with summary tables and QC plots.

precursors.<format>

This file contains precursor-level results. Each row represents one identified precursor in one run.

Main Columns

Column	Description
filename	File or run name where the precursor was identified.
precursor_index	Internal precursor index used to link rows to fragments.<format>.
modified_sequence	Peptide sequence including modifications.
stripped_sequence	Peptide sequence without modification annotations.
precursor_charge	Charge state of the precursor ion.
precursor_mz	Observed precursor mass-to-charge ratio (m/z).
rt	Observed retention time.
mobility	Observed ion mobility value, when available for the data type.
irt	Normalized retention time value.
is_decoy	Whether the row is a decoy entry.
precursor_qvalue	Precursor-level q-value.
protein_accession	Representative protein accession for the protein group.
protein_accessions	All protein accessions assigned to the protein group, separated by semicolons.
protein_names	Protein names assigned to the protein group, separated by semicolons.
protein_qvalue	Protein-level q-value.
is_proteotypic	Whether the peptide is unique to a protein group.
ms1_raw_quantity	Raw precursor-level quantity from MS1 signal, when available.
ms1_quantity	Normalized precursor-level quantity from MS1 signal, when available.
ms2_raw_quantity	Raw precursor-level quantity from fragment ion signal.
ms2_quantity	Normalized precursor-level quantity from fragment ion signal.
protein_quantity	Protein-level quantity assigned during aggregation.

Additional Columns

Some runs may include additional measurement or calibration columns depending on the input data and analysis settings.

Column	Description
empirical_mz	Calibrated library precursor m/z used during search.
empirical_rt	Calibrated library retention time used during search.
empirical_mobility	Calibrated library mobility value used during search.
elution_peak_width_rt	Elution peak width in the retention time dimension.
mobility_width	Peak width in the mobility dimension, when available.
rt_fwhm	Full width at half maximum of the RT peak, when available.
mobility_fwhm	Full width at half maximum of the mobility peak, when available.
n_aas	Number of amino acids in the peptide.
n_mods	Number of modifications in the peptide.
isotope_ints	Relative isotope intensities used for the precursor.

fragments.<format>

This file contains fragment ion-level results. Each precursor can have multiple fragment rows.

Main Columns

Column	Description
filename	File or run name where the fragment was measured.
precursor_index	Index linking the fragment row to the corresponding row in precursors.<format>.
fragment_id	Fragment identifier, usually including ion type, ion number, charge, and loss type.
fragment_mz	Fragment ion mass-to-charge ratio (m/z).
fragment_peak_area	Fragment peak area used for quantification.
fragment_normalized_peak_area	Normalized fragment peak area, when available.
is_excluded_quantification	Whether the fragment was excluded from quantification.
is_decoy	Whether the fragment belongs to a decoy entry.

Optional Annotation Columns

Column	Description
fragment_charge	Fragment ion charge.
fragment_ion_type	Fragment ion type, such as b or y.
fragment_ion	Fragment ion label, such as y7.
fragment_loss_type	Fragment neutral loss type, such as noloss, H2O, or NH3.
fragment_annotations	Combined fragment annotation string, when exported by the workflow.

Quantification Matrices

Quantification matrices summarize normalized quantities across runs.

File	Row Level	Description
peptide.matrix.<format>	Peptide	One row per peptide with run columns containing peptide-level quantities.
precursor.matrix.<format>	Precursor	One row per precursor with run columns containing precursor-level quantities.
pg.matrix.<format>	Protein group	One row per protein group with run columns containing protein group-level quantities.

The identifier and annotation columns appear first. The remaining run columns contain normalized quantity values for each file or run.

qc_report.pdf

The QC report provides a compact visual summary of the result set.

It includes an overall summary page with identification counts, coefficient of variation (CV) distribution, and protein coverage when FASTA sequences are available. Additional pages summarize each run with plots such as precursor charge distribution, precursor m/z distribution, precursor RT distribution, and protein coverage or precursors per protein.

Summary

• precursors.<format> is the main precursor-level identification and quantification report.
• fragments.<format> contains fragment ion measurements linked by precursor_index.
• peptide.matrix.<format>, precursor.matrix.<format>, and pg.matrix.<format> provide normalized quantity matrices across runs.
• qc_report.pdf provides a quick visual check of identification, quantification, and run-level QC.