masster 0.2.5__py3-none-any.whl → 0.3.1__py3-none-any.whl

masster/study/export.py

@@ -1,287 +1,674 @@
-from __future__ import annotations
-
-import os
-
-from datetime import datetime
-
-import numpy as np
-import pandas as pd
-
-
-from tqdm import tqdm
-
-from masster.spectrum import combine_peaks
-from masster.study.defaults import export_mgf_defaults
-
-
-def export_mgf(self, **kwargs):
-    """
-    Export consensus features as MGF format for database searching.
-
-    Parameters:
-        **kwargs: Keyword arguments for export parameters. Can include:
-            - An export_defaults instance to set all parameters at once
-            - Individual parameter names and values (see export_defaults for details)
-
-    Key Parameters:
-        filename (str): Output MGF file name (default: "features.mgf").
-        selection (str): "best" for first scan, "all" for every scan (default: "best").
-        split_energy (bool): Process MS2 scans by unique energy (default: True).
-        merge (bool): If selection="all", merge MS2 scans into one spectrum (default: False).
-        mz_start (float): Minimum m/z for feature selection (default: None).
-        mz_end (float): Maximum m/z for feature selection (default: None).
-        rt_start (float): Minimum RT for feature selection (default: None).
-        rt_end (float): Maximum RT for feature selection (default: None).
-        centroid (bool): Apply centroiding to spectra (default: True).
-        inty_min (float): Minimum intensity threshold (default: None).
-        deisotope (bool): Apply deisotoping to spectra (default: True).
-        verbose (bool): Enable verbose logging (default: False).
-        precursor_trim (float): Precursor trimming value (default: -10).
-        centroid_algo (str): Centroiding algorithm (default: "lmp").
-    """
-    # parameters initialization
-    params = export_mgf_defaults()
-    for key, value in kwargs.items():
-        if isinstance(value, export_mgf_defaults):
-            params = value
-            self.logger.debug("Using provided export_defaults parameters")
-        else:
-            if hasattr(params, key):
-                if params.set(key, value, validate=True):
-                    self.logger.debug(f"Updated parameter {key} = {value}")
-                else:
-                    self.logger.warning(
-                        f"Failed to set parameter {key} = {value} (validation failed)",
-                    )
-            else:
-                self.logger.debug(f"Unknown parameter {key} ignored")
-    # end of parameter initialization
-
-    # Store parameters in the Study object
-    self.store_history(["export_mgf"], params.to_dict())
-    self.logger.debug("Parameters stored to export_mgf")
-
-    # Get parameter values for use in the method
-    filename = params.get("filename")
-    selection = params.get("selection")
-    split_energy = params.get("split_energy")
-    merge = params.get("merge")
-    mz_start = params.get("mz_start")
-    mz_end = params.get("mz_end")
-    rt_start = params.get("rt_start")
-    rt_end = params.get("rt_end")
-    centroid = params.get("centroid")
-    inty_min = params.get("inty_min")
-    deisotope = params.get("deisotope")
-
-    if self.consensus_df is None:
-        self.logger.error("No consensus map found. Please run find_consensus() first.")
-        return
-    if self.consensus_ms2 is None:
-        self.logger.error("No consensus MS2 data found. Please run link_ms2() first.")
-        return
-
-    # Convert to pandas for merge operation since the result is used for groupby
-    consensus_df_pd = self.consensus_df.to_pandas()
-    consensus_ms2_pd = self.consensus_ms2.to_pandas()
-
-    features = pd.merge(
-        consensus_df_pd,
-        consensus_ms2_pd,
-        how="right",
-        on="consensus_uid",
-    )
-    if len(features) == 0:
-        self.logger.warning("No features found.")
-        return
-
-    # Pre-group by consensus_uid for fast access
-    grouped = features.groupby("consensus_uid")
-
-    def filter_peaks(spec, inty_min=None):
-        spec = spec.copy()
-        length = len(spec.mz)
-        mask = np.ones(length, dtype=bool)
-        if inty_min is not None and inty_min > 0:
-            mask = mask & (spec.inty >= inty_min)
-        for attr in spec.__dict__:
-            arr = getattr(spec, attr)
-            if (
-                isinstance(arr, list | np.ndarray)
-                and hasattr(arr, "__len__")
-                and len(arr) == length
-            ):
-                setattr(spec, attr, np.array(arr)[mask])
-        return spec
-
-    def write_ion(f, title, id, uid, mz, rt, charge, spect):
-        if spect is None:
-            return
-        f.write(f"BEGIN IONS\nTITLE={title}\n")
-        f.write(f"FEATURE_ID={id}\n")
-        f.write(f"FEATURE_UID={uid}\n")
-        f.write(f"CHARGE={charge}\nPEPMASS={mz}\nRTINSECONDS={rt}\n")
-        if spect.ms_level is None:
-            f.write("MSLEVEL=1\n")
-        else:
-            f.write(f"MSLEVEL={spect.ms_level}\n")
-        if (
-            spect.ms_level is not None
-            and spect.ms_level > 1
-            and hasattr(spect, "energy")
-        ):
-            f.write(f"ENERGY={spect.energy}\n")
-        for mz, inty in zip(spect.mz, spect.inty, strict=False):
-            f.write(f"{mz:.5f} {inty:.0f}\n")
-        f.write("END IONS\n\n")
-
-    # Prepare output path
-    if not os.path.isabs(filename):
-        if self.default_folder is not None:
-            filename = os.path.join(self.default_folder, filename)
-        else:
-            filename = os.path.join(os.getcwd(), filename)
-
-    skip = 0
-    self.logger.info(f"Exporting MGF for {len(grouped)} consensus features...")
-    with open(filename, "w", encoding="utf-8") as f:
-        tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
-        for _consensus_uid, cons_ms2 in tqdm(
-            grouped,
-            total=len(grouped),
-            desc=f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {self.log_label}Feature",
-            disable=tdqm_disable,
-        ):
-            # Use the first row for feature-level info
-            row = cons_ms2.iloc[0]
-            if mz_start is not None and row["mz"] < mz_start:
-                continue
-            if mz_end is not None and row["mz"] > mz_end:
-                continue
-            if rt_start is not None and row["rt"] < rt_start:
-                continue
-            if rt_end is not None and row["rt"] > rt_end:
-                continue
-            if len(cons_ms2) == 0:
-                skip += 1
-                continue
-
-            if split_energy:
-                energies = cons_ms2["energy"].unique()
-                for e in energies:
-                    cons_ms2_e = cons_ms2[cons_ms2["energy"] == e]
-                    if selection == "best":
-                        idx = cons_ms2_e["prec_inty"].idxmax()
-                        cons_ms2_e_row = cons_ms2_e.loc[idx]
-                        spect = cons_ms2_e_row["spec"]
-                        if spect is None:
-                            skip += 1
-                            continue
-                        if centroid:
-                            spect = spect.centroid()
-                        if deisotope:
-                            spect = spect.deisotope()
-                        spect = filter_peaks(spect, inty_min=inty_min)
-                        write_ion(
-                            f,
-                            f"uid:{cons_ms2_e_row['consensus_uid']}, rt:{cons_ms2_e_row['rt']:.2f}, mz:{cons_ms2_e_row['mz']:.4f}, energy:{e}, sample_uid:{cons_ms2_e_row['sample_uid']}, scan_id:{cons_ms2_e_row['scan_id']}",
-                            cons_ms2_e_row["consensus_id"],
-                            cons_ms2_e_row["consensus_uid"],
-                            cons_ms2_e_row["mz"],
-                            cons_ms2_e_row["rt"],
-                            round(cons_ms2_e_row["charge_mean"]),
-                            spect,
-                        )
-                    else:
-                        for row_e in cons_ms2_e.iter_rows(named=True):
-                            spect = row_e["spec"]
-                            if spect is None:
-                                continue
-                            if centroid:
-                                spect = spect.centroid()
-                            if deisotope:
-                                spect = spect.deisotope()
-                            spect = filter_peaks(spect, inty_min=inty_min)
-                            write_ion(
-                                f,
-                                f"uid:{row_e['consensus_uid']}, rt:{row_e['rt']:.2f}, mz:{row_e['mz']:.4f}, energy:{e}, sample_uid:{row_e['sample_uid']}, scanid:{row_e['scan_id']}",
-                                row_e["consensus_id"],
-                                row_e["consensus_uid"],
-                                row_e["mz"],
-                                row_e["rt"],
-                                round(row_e["charge_mean"]),
-                                spect,
-                            )
-            else:
-                if selection == "best":
-                    idx = cons_ms2["prec_inty"].idxmax()
-                    cons_ms2_e_row = cons_ms2.loc[idx]
-                    spect = cons_ms2_e_row["spec"]
-                    if spect is None:
-                        continue
-                    if centroid:
-                        spect = spect.centroid()
-                    if deisotope:
-                        spect = spect.deisotope()
-                    spect = filter_peaks(spect, inty_min=inty_min)
-                    write_ion(
-                        f,
-                        f"uid:{cons_ms2_e_row['consensus_uid']}, rt:{cons_ms2_e_row['rt']:.2f}, mz:{cons_ms2_e_row['mz']:.4f}, energy:{cons_ms2_e_row['energy']}, sample_uid:{cons_ms2_e_row['sample_uid']}, scan_id:{cons_ms2_e_row['scan_id']}",
-                        cons_ms2_e_row["consensus_id"],
-                        cons_ms2_e_row["consensus_uid"],
-                        cons_ms2_e_row["mz"],
-                        cons_ms2_e_row["rt"],
-                        round(cons_ms2_e_row["charge_mean"]),
-                        spect,
-                    )
-
-                elif selection == "all":
-                    if merge:
-                        specs = [
-                            row_e["spec"]
-                            for row_e in cons_ms2.iter_rows(named=True)
-                            if row_e["spec"] is not None
-                        ]
-                        if not specs:
-                            continue
-                        spect = combine_peaks(specs)
-                        if centroid:
-                            spect = spect.denoise()
-                            spect = spect.centroid()
-                            spect = spect.centroid()
-                        if deisotope:
-                            spect = spect.deisotope()
-                        spect = filter_peaks(spect, inty_min=inty_min)
-                        write_ion(
-                            f,
-                            f"uid:{row['consensus_uid']}, rt:{row['rt']:.2f}, mz:{row['mz']:.4f}, sample_uid:{row['sample_uid']}, scan_id:{row['scan_id']}",
-                            row["consensus_id"],
-                            row["consensus_uid"],
-                            row["mz"],
-                            row["rt"],
-                            round(row["charge_mean"]),
-                            spect,
-                        )
-                    else:
-                        for row_e in cons_ms2.iter_rows(named=True):
-                            spect = row_e["spec"]
-                            if spect is None:
-                                continue
-                            if centroid:
-                                spect = spect.centroid()
-                            if deisotope:
-                                spect = spect.deisotope()
-                            spect = filter_peaks(spect, inty_min=inty_min)
-                            write_ion(
-                                f,
-                                f"uid:{row_e['consensus_uid']}, rt:{row_e['rt']:.2f}, mz:{row_e['mz']:.4f}, energy:{row_e['energy']}, sample_uid:{row_e['sample_uid']}, scan_id:{row_e['scan_id']}",
-                                row_e["consensus_id"],
-                                row_e["consensus_uid"],
-                                row_e["mz"],
-                                row_e["rt"],
-                                round(row_e["charge_mean"]),
-                                spect,
-                            )
-        self.logger.info(
-            f"Exported {len(grouped) - skip} features to {filename}. Skipped {skip} features due to missing data.",
-        )
+from __future__ import annotations
+
+import os
+
+from datetime import datetime
+
+import numpy as np
+import pandas as pd
+import polars as pl
+
+from tqdm import tqdm
+
+from masster.spectrum import combine_peaks
+from masster.study.defaults import export_mgf_defaults
+from masster._version import get_version
+
+
+def _get_mgf_df(self, **kwargs):
+    """
+    Generate MGF data as a Polars DataFrame.
+    
+    This is the core data generation function used by export_mgf().
+    
+    Parameters:
+        **kwargs: Keyword arguments for export parameters. Same as export_mgf() 
+                 except return_data is not relevant here.
+    
+    Returns:
+        pl.DataFrame: DataFrame with columns:
+            - mgf_index: MGF index
+            - title: MGF title string
+            - feature_id: Consensus feature ID
+            - feature_uid: Consensus feature UID
+            - charge: Charge state
+            - pepmass: Precursor m/z
+            - rtinseconds: Retention time in seconds
+            - mslevel: MS level
+            - type: Spectrum type (e.g., "MS2")
+            - energy: Collision energy (if available)
+            - spec_len: Number of peaks in spectrum
+            - spec_mz: List of spectrum m/z values
+            - spec_int: List of spectrum intensity values
+    """
+    # parameters initialization
+    params = export_mgf_defaults()
+    for key, value in kwargs.items():
+        if isinstance(value, export_mgf_defaults):
+            params = value
+            self.logger.debug("Using provided export_defaults parameters")
+        else:
+            if hasattr(params, key):
+                if params.set(key, value, validate=True):
+                    self.logger.debug(f"Updated parameter {key} = {value}")
+                else:
+                    self.logger.warning(
+                        f"Failed to set parameter {key} = {value} (validation failed)",
+                    )
+            else:
+                self.logger.debug(f"Unknown parameter {key} ignored")
+    # end of parameter initialization
+
+    # Store parameters in the Study object
+    self.store_history(["get_mgf"], params.to_dict())
+    self.logger.debug("Parameters stored to get_mgf")
+
+    # Get parameter values for use in the method
+    selection = params.get("selection")
+    split_energy = params.get("split_energy")
+    merge = params.get("merge")
+    mz_start = params.get("mz_start")
+    mz_end = params.get("mz_end")
+    rt_start = params.get("rt_start")
+    rt_end = params.get("rt_end")
+    centroid = params.get("centroid")
+    inty_min = params.get("inty_min")
+    deisotope = params.get("deisotope")
+
+    if self.consensus_df is None:
+        self.logger.error("No consensus map found. Please run merge() first.")
+        return None
+    if self.consensus_ms2 is None:
+        self.logger.error("No consensus MS2 data found. Please run link_ms2() first.")
+        return None
+
+    # Convert to pandas for merge operation since the result is used for groupby
+    consensus_df_pd = self.consensus_df.to_pandas()
+    consensus_ms2_pd = self.consensus_ms2.to_pandas()
+
+    features = pd.merge(
+        consensus_df_pd,
+        consensus_ms2_pd,
+        how="right",
+        on="consensus_uid",
+    )
+    if len(features) == 0:
+        self.logger.warning("No features found.")
+        return pl.DataFrame()
+
+    # Pre-group by consensus_uid for fast access
+    grouped = features.groupby("consensus_uid")
+
+    def filter_peaks(spec, inty_min=None):
+        spec = spec.copy()
+        length = len(spec.mz)
+        mask = np.ones(length, dtype=bool)
+        if inty_min is not None and inty_min > 0:
+            mask = mask & (spec.inty >= inty_min)
+        for attr in spec.__dict__:
+            arr = getattr(spec, attr)
+            if isinstance(arr, list | np.ndarray) and hasattr(arr, "__len__") and len(arr) == length:
+                setattr(spec, attr, np.array(arr)[mask])
+        return spec
+
+    def create_ion_dict(title, id, uid, mz, rt, charge, spect, mgf_id):
+        """Create a dictionary representing an ion for the DataFrame."""
+        if spect is None:
+            return None
+        
+        # Prepare spectrum data
+        spectrum_mz = spect.mz.tolist() if hasattr(spect.mz, 'tolist') else list(spect.mz)
+        spectrum_inty = spect.inty.tolist() if hasattr(spect.inty, 'tolist') else list(spect.inty)
+        
+        # Determine MS level
+        ms_level = spect.ms_level if spect.ms_level is not None else 1
+        
+        # Get energy if available
+        energy = getattr(spect, 'energy', None)
+        
+        # Determine spectrum type based on MS level
+        spec_type = f"MS{ms_level}" if ms_level > 1 else "MS1"
+        
+        # Calculate spectrum length
+        spec_len = len(spectrum_mz)
+        
+        return {
+            'mgf_index': mgf_id,
+            'title': title,
+            'feature_id': id,
+            'feature_uid': uid,
+            'charge': charge,
+            'pepmass': mz,
+            'rtinseconds': rt,
+            'mslevel': ms_level,
+            'type': spec_type,
+            'energy': energy,
+            'spec_len': spec_len,
+            'spec_mz': spectrum_mz,
+            'spec_int': spectrum_inty,
+        }
+
+    # Collect all ion data
+    ion_data = []
+    skip = 0
+    mgf_counter = 0
+    self.logger.info(f"Generating MGF data for {len(grouped)} consensus features...")
+    
+    tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
+    for _consensus_uid, cons_ms2 in tqdm(
+        grouped,
+        total=len(grouped),
+        desc=f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {self.log_label}Feature",
+        disable=tdqm_disable,
+    ):
+        # Use the first row for feature-level info
+        row = cons_ms2.iloc[0]
+        if mz_start is not None and row["mz"] < mz_start:
+            continue
+        if mz_end is not None and row["mz"] > mz_end:
+            continue
+        if rt_start is not None and row["rt"] < rt_start:
+            continue
+        if rt_end is not None and row["rt"] > rt_end:
+            continue
+        if len(cons_ms2) == 0:
+            skip += 1
+            continue
+
+        if split_energy:
+            energies = cons_ms2["energy"].unique()
+            for e in energies:
+                cons_ms2_e = cons_ms2[cons_ms2["energy"] == e]
+                if selection == "best":
+                    idx = cons_ms2_e["prec_inty"].idxmax()
+                    cons_ms2_e_row = cons_ms2_e.loc[idx]
+                    spect = cons_ms2_e_row["spec"]
+                    if spect is None:
+                        skip += 1
+                        continue
+                    if centroid:
+                        spect = spect.centroid()
+                    if deisotope:
+                        spect = spect.deisotope()
+                    spect = filter_peaks(spect, inty_min=inty_min)
+                    mgf_counter += 1
+                    ion_dict = create_ion_dict(
+                        f"uid:{cons_ms2_e_row['consensus_uid']}, rt:{cons_ms2_e_row['rt']:.2f}, mz:{cons_ms2_e_row['mz']:.4f}, energy:{e}, sample_uid:{cons_ms2_e_row['sample_uid']}, scan_id:{cons_ms2_e_row['scan_id']}",
+                        cons_ms2_e_row["consensus_id"],
+                        cons_ms2_e_row["consensus_uid"],
+                        cons_ms2_e_row["mz"],
+                        cons_ms2_e_row["rt"],
+                        round(cons_ms2_e_row["charge_mean"]),
+                        spect,
+                        mgf_counter,
+                    )
+                    if ion_dict is not None:
+                        ion_data.append(ion_dict)
+                else:
+                    for row_e in cons_ms2_e.iter_rows(named=True):
+                        spect = row_e["spec"]
+                        if spect is None:
+                            continue
+                        if centroid:
+                            spect = spect.centroid()
+                        if deisotope:
+                            spect = spect.deisotope()
+                        spect = filter_peaks(spect, inty_min=inty_min)
+                        mgf_counter += 1
+                        ion_dict = create_ion_dict(
+                            f"uid:{row_e['consensus_uid']}, rt:{row_e['rt']:.2f}, mz:{row_e['mz']:.4f}, energy:{e}, sample_uid:{row_e['sample_uid']}, scanid:{row_e['scan_id']}",
+                            row_e["consensus_id"],
+                            row_e["consensus_uid"],
+                            row_e["mz"],
+                            row_e["rt"],
+                            round(row_e["charge_mean"]),
+                            spect,
+                            mgf_counter,
+                        )
+                        if ion_dict is not None:
+                            ion_data.append(ion_dict)
+        else:
+            if selection == "best":
+                idx = cons_ms2["prec_inty"].idxmax()
+                cons_ms2_e_row = cons_ms2.loc[idx]
+                spect = cons_ms2_e_row["spec"]
+                if spect is None:
+                    continue
+                if centroid:
+                    spect = spect.centroid()
+                if deisotope:
+                    spect = spect.deisotope()
+                spect = filter_peaks(spect, inty_min=inty_min)
+                mgf_counter += 1
+                ion_dict = create_ion_dict(
+                    f"uid:{cons_ms2_e_row['consensus_uid']}, rt:{cons_ms2_e_row['rt']:.2f}, mz:{cons_ms2_e_row['mz']:.4f}, energy:{cons_ms2_e_row['energy']}, sample_uid:{cons_ms2_e_row['sample_uid']}, scan_id:{cons_ms2_e_row['scan_id']}",
+                    cons_ms2_e_row["consensus_id"],
+                    cons_ms2_e_row["consensus_uid"],
+                    cons_ms2_e_row["mz"],
+                    cons_ms2_e_row["rt"],
+                    round(cons_ms2_e_row["charge_mean"]),
+                    spect,
+                    mgf_counter,
+                )
+                if ion_dict is not None:
+                    ion_data.append(ion_dict)
+
+            elif selection == "all":
+                if merge:
+                    specs = [row_e["spec"] for row_e in cons_ms2.iter_rows(named=True) if row_e["spec"] is not None]
+                    if not specs:
+                        continue
+                    spect = combine_peaks(specs)
+                    if centroid:
+                        spect = spect.denoise()
+                        spect = spect.centroid()
+                    if deisotope:
+                        spect = spect.deisotope()
+                    spect = filter_peaks(spect, inty_min=inty_min)
+                    mgf_counter += 1
+                    ion_dict = create_ion_dict(
+                        f"uid:{row['consensus_uid']}, rt:{row['rt']:.2f}, mz:{row['mz']:.4f}, sample_uid:{row['sample_uid']}, scan_id:{row['scan_id']}",
+                        row["consensus_id"],
+                        row["consensus_uid"],
+                        row["mz"],
+                        row["rt"],
+                        round(row["charge_mean"]),
+                        spect,
+                        mgf_counter,
+                    )
+                    if ion_dict is not None:
+                        ion_data.append(ion_dict)
+                else:
+                    for row_e in cons_ms2.iter_rows(named=True):
+                        spect = row_e["spec"]
+                        if spect is None:
+                            continue
+                        if centroid:
+                            spect = spect.centroid()
+                        if deisotope:
+                            spect = spect.deisotope()
+                        spect = filter_peaks(spect, inty_min=inty_min)
+                        mgf_counter += 1
+                        ion_dict = create_ion_dict(
+                            f"uid:{row_e['consensus_uid']}, rt:{row_e['rt']:.2f}, mz:{row_e['mz']:.4f}, energy:{row_e['energy']}, sample_uid:{row_e['sample_uid']}, scan_id:{row_e['scan_id']}",
+                            row_e["consensus_id"],
+                            row_e["consensus_uid"],
+                            row_e["mz"],
+                            row_e["rt"],
+                            round(row_e["charge_mean"]),
+                            spect,
+                            mgf_counter,
+                        )
+                        if ion_dict is not None:
+                            ion_data.append(ion_dict)
+
+    self.logger.debug(f"Generated MGF data for {len(ion_data)} spectra")
+    self.logger.debug(f"Skipped {skip} features due to missing data.")
+
+    # Convert to Polars DataFrame
+    if not ion_data:
+        return pl.DataFrame()
+    
+    return pl.DataFrame(ion_data)
+
+
+def export_mgf(self, **kwargs):
+    """
+    Export consensus features as MGF format for database searching.
+
+    Parameters:
+        **kwargs: Keyword arguments for export parameters. Can include:
+            - An export_defaults instance to set all parameters at once
+            - Individual parameter names and values (see export_defaults for details)
+
+    Key Parameters:
+        filename (str): Output MGF file name (default: "features.mgf").
+        selection (str): "best" for first scan, "all" for every scan (default: "best").
+        split_energy (bool): Process MS2 scans by unique energy (default: True).
+        merge (bool): If selection="all", merge MS2 scans into one spectrum (default: False).
+        mz_start (float): Minimum m/z for feature selection (default: None).
+        mz_end (float): Maximum m/z for feature selection (default: None).
+        rt_start (float): Minimum RT for feature selection (default: None).
+        rt_end (float): Maximum RT for feature selection (default: None).
+        centroid (bool): Apply centroiding to spectra (default: True).
+        inty_min (float): Minimum intensity threshold (default: None).
+        deisotope (bool): Apply deisotoping to spectra (default: True).
+        verbose (bool): Enable verbose logging (default: False).
+        precursor_trim (float): Precursor trimming value (default: -10).
+        centroid_algo (str): Centroiding algorithm (default: "lmp").
+        
+    Returns:
+        None: Writes MGF file to disk.
+    """
+    # Get mgf data as DataFrame
+    mgf_data = self._get_mgf_df(**kwargs)
+    
+    if mgf_data is None or len(mgf_data) == 0:
+        self.logger.warning("No MGF data generated.")
+        return
+
+    # Get filename from parameters
+    params = export_mgf_defaults()
+    for key, value in kwargs.items():
+        if isinstance(value, export_mgf_defaults):
+            params = value
+        else:
+            if hasattr(params, key):
+                params.set(key, value, validate=True)
+    
+    filename = params.get("filename")
+    
+    # Prepare output path
+    if not os.path.isabs(filename):
+        if self.folder is not None:
+            filename = os.path.join(self.folder, filename)
+        else:
+            filename = os.path.join(os.getcwd(), filename)
+
+    # Write MGF file
+    with open(filename, "w", encoding="utf-8") as f:
+        for row in mgf_data.iter_rows(named=True):
+            # Write BEGIN IONS
+            f.write("BEGIN IONS\n")
+            
+            # Write metadata
+            if row["mgf_index"] is not None:
+                f.write(f"INDEX={row['mgf_index']}\n")
+            f.write(f"TITLE={row['title']}\n")
+            f.write(f"FEATURE_ID={row['feature_id']}\n")
+            f.write(f"FEATURE_UID={row['feature_uid']}\n")
+            f.write(f"CHARGE={row['charge']}\n")
+            f.write(f"PEPMASS={row['pepmass']}\n")
+            f.write(f"RTINSECONDS={row['rtinseconds']}\n")
+            f.write(f"MSLEVEL={row['mslevel']}\n")
+            
+            if row["energy"] is not None:
+                f.write(f"ENERGY={row['energy']}\n")
+            
+            # Write spectrum data
+            spectrum_mz = row["spec_mz"]
+            spectrum_inty = row["spec_int"]
+            for mz_val, inty in zip(spectrum_mz, spectrum_inty, strict=False):
+                f.write(f"{mz_val:.5f} {inty:.0f}\n")
+            
+            # Write END IONS
+            f.write("END IONS\n\n")
+    
+    self.logger.info(f"Exported {len(mgf_data)} spectra to {filename}")
+
+
+def export_mztab(self, filename: str = None, include_mgf=True, **kwargs) -> None:
+    """
+    Export the study as a fully compliant mzTab-M file.
+
+    Args:
+        filename (str, optional): Path to the output mzTab-M file.
+        title (str, optional): Human-readable title for the file.
+        description (str, optional): Human-readable description.
+        **kwargs: Additional metadata or export options.
+    """
+    if filename is None:
+        filename = "study.mztab"
+    if not os.path.isabs(filename):
+        if self.folder is not None:
+            filename = os.path.join(self.folder, filename)
+        else:
+            filename = os.path.join(os.getcwd(), filename)
+    
+    # get mgf data
+    mgf_data = self._get_mgf_df(**kwargs)
+    # Create mapping from feature_uid to MGF indexes
+    mgf_mapping: dict[str, list[int]] = {}
+    if mgf_data is not None and len(mgf_data) > 0:
+        for row in mgf_data.iter_rows(named=True):
+            feature_uid = row['feature_uid']
+            mgf_index = row['mgf_index']
+            if feature_uid not in mgf_mapping:
+                mgf_mapping[feature_uid] = []
+            mgf_mapping[feature_uid].append(mgf_index)
+    
+    # --- Prepare MTD (metadata) section ---
+    mtd_lines = []
+    mtd_lines.append(f"COM file generated by MASSter on {datetime.now().strftime('%Y-%m-%d %H:%M:%S')}")
+    mtd_lines.append("\nMTD\tmzTab-version\t2.2.0-M")
+    id = self.label if self.label else self.folder
+    mtd_lines.append(f"MTD\tmzTab-id\t{id}")
+    mtd_lines.append('')
+    mtd_lines.append("MTD\tcv[1]-label\tMS")
+    mtd_lines.append("MTD\tcv[1]-full_name\tPSI-MS controlled vocabulary")
+    mtd_lines.append("MTD\tcv[1]-version\t4.1.199")
+    mtd_lines.append("MTD\tcv[1]-uri\thttps://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo")
+    mtd_lines.append('')
+    mtd_lines.append("MTD\tsmall_molecule-quantification_unit\t[MS, MS:1001844, MS1 feature area, ]")
+    mtd_lines.append("MTD\tsmall_molecule_feature-quantification_unit\t[MS, MS:1001844, MS1 feature area, ]")
+    mtd_lines.append("MTD\tsmall_molecule-identification_reliability\t[MS, MS:1002955, hr-ms compound identification confidence level, ]")
+    mtd_lines.append("MTD\tid_confidence_measure[1]\t[MS, MS:1002888, small molecule confidence measure, ]")
+    mtd_lines.append('')
+    mtd_lines.append("MTD\tsoftware[1]\t[MS, MS:1003430, OpenMS, unknown]")
+    mtd_lines.append(f"MTD\tsoftware[2]\t[MS, MS:1002878, MASSter, {get_version()}]")
+    mtd_lines.append("MTD\tquantification_method\t[MS, MS:1001834, LC-MS label-free quantitation analysis, ]")
+    mtd_lines.append('')
+    mtd_lines.append("MTD\tdatabase[1]\t[, , \"no database\", null]")
+    mtd_lines.append("MTD\tdatabase[1]-prefix\tnull")
+    mtd_lines.append("MTD\tdatabase[1]-version\tUnknown")
+    mtd_lines.append("MTD\tdatabase[1]-uri\tnull")
+    #mtd_lines.append('')
+    for i, row in enumerate(self.samples_df.iter_rows(named=True), 1):
+        mtd_lines.append(f"\nMTD\tsample[{i}]\t{row.get('sample_uid', f'sample_{i}')}")
+        mtd_lines.append(f"MTD\tsample[{i}]-description\t{row.get('sample_name', 'unknown')}")
+        mtd_lines.append(f"MTD\tms_run[{i}]-location\tfile://{row.get('sample_path', 'unknown')}")
+        mtd_lines.append(f"MTD\tassay[{i}]\tAssay_{i}")
+        mtd_lines.append(f"MTD\tassay[{i}]-sample_ref\tsample[{i}]")
+        mtd_lines.append(f"MTD\tassay[{i}]-ms_run_ref\tms_run[{i}]")
+    mtd_lines.append('')
+    mtd_lines.append("MTD\tstudy_variable[1]\tundefined")
+    mtd_lines.append("MTD\tstudy_variable[1]_refs\tundefined")
+    #assay_refs = '|'.join([f"assay[{i}]" for i in range(1, len(self.samples_df)+1)])
+    #mtd_lines.append(f"MTD\tstudy_variable[1]-assay_refs\t{assay_refs}")
+    #mtd_lines.append("MTD\tstudy_variable[1]-description\tAll assays grouped (default)")
+    with open(filename, 'w', encoding='utf-8') as f:
+        for line in mtd_lines:
+            f.write(line + '\n')
+
+    # --- SML (Small Molecule) table ---
+    sml_lines = []
+    sml_header = [
+        "SMH",
+        "SML_ID",
+        "SMF_ID_REFS",
+        "database_identifier",
+        "chemical_formula",
+        "smiles",
+        "inchi",
+        "chemical_name",
+        "uri",
+        "theoretical_neutral_mass",
+        "adduct_ions",
+        "reliability",
+        "best_id_confidence_measure",
+        "best_id_confidence_value",
+        "opt_global_mgf_index",        
+    ]
+    
+    abundance_matrix = self.get_consensus_matrix()
+    # Use the matrix as-is since it already has the correct sample columns
+    # The matrix columns are sample names, which is what we want for the assay columns
+    
+    # round to int
+    abundance_matrix = abundance_matrix.round(0)
+
+    # Use actual number of samples from the abundance matrix
+    n_assays = len(abundance_matrix.columns)
+    sml_header += [f"abundance_assay[{i}]" for i in range(1, n_assays+1)]
+    sml_header += ["abundance_study_variable[1]", "abundance_variation_study_variable[1]"]
+    sml_lines.append('\t'.join(sml_header))
+
+    # get adducts from consensus_df['adducts']. If value is None or [], use 'null'. If there is, take the first element and the first string
+    adduct_list = []
+    mapping = {'H1': '[M+H]+', 'H2': '[M+2H]2+', 
+               'Na1': '[M+Na]+', 'Na2': '[M+2Na]2+',
+               'NH4': '[M+NH4]+', 'HCOO': '[M+HCOO]-', 
+               'CH3COO': '[M+CH3COO]-', 'H2O': '[M+H2O]+',
+               'HCO2': '[M+HCO2]-', 'H3PO4': '[M+H3PO4]+',
+               'H3O1': '[M+H3O]+', 'K1': '[M+K]+',
+               'H4N1': '[M+NH4]+', 
+               'H-1': '[M-H]-', 'Cl1': '[M+Cl]-',
+               'Br1': '[M+Br]-', 'I1': '[M+I]-',
+               'H2O2': '[M+H2O2]+', 'H3O2': '[M+H3O2]+',}
+    for idx, row in enumerate(self.consensus_df.iter_rows(named=True), 1):
+        adduct = 'null'
+        if 'adducts' in row:
+            row_adducts = row['adducts']
+            if isinstance(row_adducts, list) and row_adducts:
+                # Each adduct is a dictionary with 'adduct' key
+                first_adduct_dict = row_adducts[0]
+                if isinstance(first_adduct_dict, dict) and 'adduct' in first_adduct_dict:
+                    adduct_str = first_adduct_dict['adduct']
+                    if adduct_str in mapping:
+                        adduct = mapping[adduct_str]
+                    else:
+                        adduct = adduct_str
+
+        adduct_list.append(adduct)
+
+    for idx, row in enumerate(self.consensus_df.iter_rows(named=True), 1):
+        # Get MGF indexes for this consensus feature
+        mgf_indexes = mgf_mapping.get(row['consensus_uid'], [])
+        
+        sml_row = [
+            "SML",
+            str(idx),
+            str(idx),
+            str(row.get('database_identifier', 'null')),
+            str(row.get('chemical_formula', 'null')),
+            str(row.get('smiles', 'null')),
+            str(row.get('inchi', 'null')),
+            str(row.get('chemical_name', 'null')),
+            str(row.get('uri', 'null')),
+            str(row.get('theoretical_neutral_mass', 'null')),
+            adduct_list[idx-1],
+            str(row.get('reliability', 'null')),            
+            str(row.get('best_id_confidence_measure', 'null')),
+            str(row.get('best_id_confidence_value', 'null')),
+            ','.join(map(str, mgf_indexes)) if mgf_indexes else 'null',
+        ]
+        # Add abundance values for each assay
+        consensus_uid = row['consensus_uid']
+        if consensus_uid in abundance_matrix.index:
+            abundance_values = abundance_matrix.loc[consensus_uid].tolist()
+            sml_row += [str(val) if pd.notna(val) else 'null' for val in abundance_values]
+        else:
+            sml_row += ['null'] * n_assays
+        sml_row += ['null', 'null']
+        sml_lines.append('\t'.join(sml_row))
+    with open(filename, 'a', encoding='utf-8') as f:
+        f.write('\n')
+        for line in sml_lines:
+            f.write(line + '\n')
+
+    # --- SMF (Small Molecule Feature) table ---
+    smf_lines = []
+    smf_header = [
+        "SFH",
+        "SMF_ID",
+        "SME_ID_REFS",
+        "SME_ID_REF_ambiguity_code",
+        "adduct_ion",
+        "isotopomer",
+        "exp_mass_to_charge",
+        "charge",
+        "retention_time_in_seconds",
+        "retention_time_in_seconds_start",
+        "retention_time_in_seconds_end",
+    ]
+    smf_header += [f"abundance_assay[{i}]" for i in range(1, n_assays+1)]
+    smf_lines.append('\t'.join(smf_header))
+    
+    # SMF table uses the same consensus features as SML, just different metadata
+    for idx, row in enumerate(self.consensus_df.iter_rows(named=True), 1):
+        smf_row = [
+            "SMF",
+            str(idx),
+            "null",
+            "null",
+            adduct_list[idx-1],  # adduct_ion
+            str(row.get('isotopomer', 'null')),
+            str(row.get('mz', 'null')),  # exp_mass_to_charge
+            str(row.get('charge', 'null')),
+            str(row.get('rt', 'null')),  # retention_time_in_seconds
+            str(row.get('retention_time_in_seconds_start', 'null')),
+            str(row.get('retention_time_in_seconds_end', 'null')),
+        ]
+        # Add abundance values for each assay - same as SML
+        consensus_uid = row['consensus_uid']
+        if consensus_uid in abundance_matrix.index:
+            abundance_values = abundance_matrix.loc[consensus_uid].tolist()
+            smf_row += [str(val) if pd.notna(val) else 'null' for val in abundance_values]
+        else:
+            smf_row += ['null'] * n_assays
+        smf_lines.append('\t'.join(smf_row))
+    with open(filename, 'a', encoding='utf-8') as f:
+        f.write('\n')
+        for line in smf_lines:
+            f.write(line + '\n')
+
+    # --- MGF table ---
+    if include_mgf and mgf_data is not None and len(mgf_data) > 0:
+        mgf_lines = []
+        # Header
+        mgf_header = [
+            "COM",
+            "MGH", 
+            "mgf_id",
+            "prec_id", 
+            "prec_rt",
+            "prec_mz",
+            "prec_int",
+            "energy",
+            "level",
+            "title",
+            "spec_tic",
+            "spec_len",
+            "spec_mz",
+            "spec_int"
+        ]
+        mgf_lines.append('\t'.join(mgf_header))
+        
+        # Data rows
+        for row in mgf_data.iter_rows(named=True):
+            # Calculate spectrum TIC (total ion current) from the spectrum data
+            spectrum_mz = row["spec_mz"]
+            spectrum_inty = row["spec_int"]
+            spec_tic = sum(spectrum_inty) if spectrum_inty else 0
+            spec_len = row["spec_len"] if row["spec_len"] is not None else 0
+            
+            # Format spectrum data as pipe-separated strings
+            spec_mz_str = '|'.join([f"{mz:.4f}" for mz in spectrum_mz]) if spectrum_mz else ""
+            spec_int_str = '|'.join([f"{int(inty)}" for inty in spectrum_inty]) if spectrum_inty else ""
+            
+            mgf_row = [
+                "COM",
+                "MGF",
+                str(row["mgf_index"]) if row["mgf_index"] is not None else "null",
+                str(row["feature_id"]) if row["feature_id"] is not None else "null",
+                f"{row['rtinseconds']:.2f}" if row["rtinseconds"] is not None else "null",
+                f"{row['pepmass']:.4f}" if row["pepmass"] is not None else "null",
+                "null",  # prec_int - not available in current data
+                str(row["energy"]) if row["energy"] is not None else "null",
+                str(row["mslevel"]) if row["mslevel"] is not None else "null",
+                str(row["title"]) if row["title"] is not None else "null",
+                f"{int(spec_tic)}" if spec_tic > 0 else "null",
+                str(spec_len) if spec_len > 0 else "null",
+                spec_mz_str if spec_mz_str else "null",
+                spec_int_str if spec_int_str else "null"
+            ]
+            mgf_lines.append('\t'.join(mgf_row))
+        
+        # Write MGF table
+        with open(filename, 'a', encoding='utf-8') as f:
+            f.write('\n')
+            for line in mgf_lines:
+                f.write(line + '\n')
+
+    if include_mgf:    
+        self.logger.info(f"Exported mzTab-M to {filename}")