precursors.csv
This file contains comprehensive precursor-level results with each row representing a single identified precursor ion.
Column Description
| Column | Description |
|---|---|
elution_peak_width_rt |
Elution peak width based on retention time (seconds). |
frame_scan_correlation |
Correlation between frame and scan dimensions. |
rt_fwhm |
Full Width at Half Maximum (FWHM) of the RT peak. |
mobility_fwhm |
FWHM of the mobility peak. |
rt |
Observed retention time (seconds). |
mobility |
Observed mobility value. |
precursor_mz |
Observed precursor mass-to-charge ratio (m/z). |
mobility_width |
Window width in the mobility (drift time) dimension. |
precursor_index |
Internal index of the precursor (links to fragments). |
is_decoy |
Whether the precursor is a decoy entry. |
modified_sequence |
Peptide sequence including modifications. |
precursor_charge |
Charge state of the precursor ion. |
irt |
Indexed Retention Time (iRT) value. |
n_aas |
Number of amino acids in the peptide. |
n_mods |
Number of modifications in the peptide. |
empirical_mz |
The library m/z value after calibration to experimental conditions. |
isotope_ints |
Relative intensities of isotope peaks. |
empirical_rt |
The library retention time after calibration to experimental conditions. |
empirical_mobility |
The library mobility value after calibration to experimental conditions. |
protein_accessions |
Protein accession IDs associated with the precursor. |
delta_rt |
Difference between observed and predicted RT. |
n_lys |
Number of lysine (K) residues. |
n_arg |
Number of arginine (R) residues. |
n_pro |
Number of proline (P) residues. |
precursor_proba |
Probability score for precursor identification. |
precursor_qvalue |
Precursor-level q-value (FDR-corrected). |
filename |
Name of the file/run where the precursor was detected. |
protein_group |
Representative accession of the protein group. |
protein_groups |
All protein groups containing this precursor. |
protein_qvalue |
Protein-level q-value (FDR-corrected). |
ms2_raw_quantity |
Raw MS2 intensity. |
ms2_quantity |
Normalized MS2 intensity. |
protein_quantity |
Calculated protein-level quantification. |
fragments.csv
This file contains fragment ion–level data associated with each precursor.
Each precursor may have multiple fragments corresponding to individual fragment ions.
Column Description
| Column | Description |
|---|---|
precursor_index |
Index linking to the corresponding precursor in precursors.csv. |
fragment_id |
Unique identifier of the fragment. |
is_decoy |
Whether the fragment is a decoy. |
filename |
File/run where the fragment was detected. |
fragment_peak_area |
Fragment peak area (intensity). |
fragment_mz |
Fragment mass-to-charge ratio (m/z). |
Quantification Matrices (*.matrix.csv)
Quantification matrix at precursor or protein level.
Rows are IDs (precursor or protein).
Columns are filenames (runs) with measured values (usually normalized intensity).
File Format
- Each row represents a unique precursor or protein.
- Each column represents a filename (run).
- Cell values contain the measured normalized intensity.
Columns
| Column | Description |
|---|---|
<id> |
Unique precursor or protein identifier. |
<filename> |
Normalized quantification value measured in that file/run. |
Summary
precursors.csv: Main table linking identification, prediction, and quantification at the precursor level.fragments.csv: Detailed fragment ion information, linked viaprecursor_index.*.matrix.csv: Quantitative matrices summarizing normalized values across runs.
These files together provide complete traceability from fragment ions → precursors → proteins, enabling robust downstream analysis, visualization, and statistical inference.