Update README.md

README.md

@@ -83,23 +83,23 @@ winnow predict \
 ## Inputs and outputs
 **Required columns for calibration:**
 - Spectrum data (*.parquet)
-  - spectrum_id (string): unique spectrum identifier
-  - sequence (string): ground truth peptide sequence from database search (optional)
-  - retention_time (float): retention time (seconds)
-  - precursor_mass (float): mass of the precursor ion (from MS1)
-  - mz_array (list[float]): mass-to-charge values of the MS2 spectrum
-  - intensity_array (list[float]): intensity values of the MS2 spectrum
-  - precursor_charge (int): charge of the precursor (from MS1)
+  - `spectrum_id` (string): unique spectrum identifier
+  - `sequence` (string): ground truth peptide sequence from database search (optional)
+  - `retention_time` (float): retention time (seconds)
+  - `precursor_mass` (float): mass of the precursor ion (from MS1)
+  - `mz_array` (list[float]): mass-to-charge values of the MS2 spectrum
+  - `intensity_array` (list[float]): intensity values of the MS2 spectrum
+  - `precursor_charge` (int): charge of the precursor (from MS1)
 
 - Beam predictions (*_beams.csv)
-  - spectrum_id (string)
-  - sequence (string): ground truth peptide sequence from database search (optional)
-  - preds (string): top prediction, untokenised sequence
-  - preds_tokenised (string): comma‐separated tokens for the top prediction
-  - log_probs (float): top prediction log probability
-  - preds_beam_k (string): untokenised sequence for beam k (k≥0)
-  - log_probs_beam_k (float)
-  - token_log_probs_k (string/list-encoded): per-token log probabilities for beam k
+  - `spectrum_id` (string)
+  - `sequence` (string): ground truth peptide sequence from database search (optional)
+  - `preds` (string): top prediction, untokenised sequence
+  - `preds_tokenised` (string): comma‐separated tokens for the top prediction
+  - `log_probs` (float): top prediction log probability
+  - `preds_beam_k` (string): untokenised sequence for beam k (k≥0)
+  - `log_probs_beam_k` (float)
+  - `token_log_probs_k` (string/list-encoded): per-token log probabilities for beam k
 
 **Output columns (added by Winnow's calibrator on `predict`):**
   - `calibrated_confidence`: calibrated probability