masster 0.4.22__tar.gz → 0.5.1__tar.gz

{masster-0.4.22 → masster-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.22
+Version: 0.5.1
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -686,6 +686,7 @@ Requires-Dist: bokeh>=3.7.3
 Requires-Dist: cmap>=0.6.2
 Requires-Dist: datashader>=0.18.1
 Requires-Dist: h5py>=3.14.0
+Requires-Dist: hdbscan>=0.8.40
 Requires-Dist: holoviews>=1.21.0
 Requires-Dist: hvplot>=0.11.3
 Requires-Dist: loguru>=0.7.3
@@ -701,6 +702,7 @@ Requires-Dist: pythonnet>=3.0.0
 Requires-Dist: scikit-learn>=1.7.1
 Requires-Dist: scipy>=1.12.0
 Requires-Dist: tqdm>=4.65.0
+Requires-Dist: umap-learn>=0.5.9.post2
 Provides-Extra: dev
 Requires-Dist: bandit>=1.7.0; extra == 'dev'
 Requires-Dist: black>=23.0.0; extra == 'dev'
@@ -726,12 +728,13 @@ Description-Content-Type: text/markdown
 
 # MASSter
 
-**MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. 
+**MASSter** is a Python package for the analysis of mass spectrometry data, tailored for the purpose of metabolomics and LC-MS data processing. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. The sample-centric feature detection uses OpenMS. All other functionalities for e.g. centroiding, RT alignment, adduct and isotopomer detection, merging of multiple samples, gap-filling, quantification, etc. were redesigned and engineered to maximize scalability (tested with 3000 LC-MS), speed, quality, and results.
 
 This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. 
 
-Some of the core processing functions are derived from OpenMS. We use the same nomenclature and refer to their documentation for an explanation of the parameters. To a large extent, however, you should be able to use the defaults (=no parameters) when calling processing steps.
+## Prerequisites
 
+**MASSter** reads raw (Thermo), wiff (SCIEX), or mzML data. It's recommended to provide raw, profile data.
 
 ## Installation
 
@@ -739,20 +742,60 @@ Some of the core processing functions are derived from OpenMS. We use the same n
 pip install masster
 ```
 
-### Basic Workflow for analyzing LC-MS study with 2-... samples
+## Basic usage
+### Quick start: use the wizard
+
+```python
+import masster
+masster.wizard.execute(
+    source=r'..\..\folder_with_raw_data',
+    folder=r'..\..folder_to_store_results'
+    )
+```
 
+This will run a wizard that should perform all key steps and save the results to the `folder`.
+
+### Basic workflow for analyzing a single sample
 ```python
 import masster
+sample = masster.Sample(filename='...') # full path to a *.raw, *.wiff, or *.mzML file
+# process
+sample.find_features(chrom_fwhm=0.5, noise=50) # for orbitrap data, set noise to 1e5
+sample.find_adducts()
+sample.find_ms2()
+
+# access data
+sample.features_df
+
+# save results
+sample.save() # stores to *.sample5, our custom hdf5 format
+sample.export_mgf()
+
+# some plots
+sample.plot_bpc()
+sample.plot_tic()
+sample.plot_2d()
+sample.plot_features_stats()
+
+# explore methods
+dir(study)
+```
+
+### Basic Workflow for analyzing LC-MS study with 2-... samples
 
+```python
+import masster
 # Initialize the Study object with the default folder
-study = masster.Study(default_folder=r'D:\...\mylcms')
+study = masster.Study(folder=r'D:\...\mylcms')
 
 # Load data from folder with raw data, here: WIFF
 study.add(r'D:\...\...\...\*.wiff')
 
 # Perform retention time correction
-study.align(rt_max_diff=2.0)
+study.align(rt_tol=2.0)
 study.plot_alignment()
+study.plot_bpc()
+study.plot_rt_correction()
 
 # Find consensus features
 study.merge(min_samples=3)
@@ -772,18 +815,15 @@ study.export_parquet()
 
 # Save the study to .study5
 study.save()
-```
-
-## Requirements
 
-- Python ≥ 3.11
-- Key dependencies: pandas, polars, numpy, scipy, matplotlib, bokeh, holoviews, panel
-- See `pyproject.toml` for complete dependency list
+# Some of the plots...
+study.plot_samples_pca()
+study.plot_samples_umap()
+study.plot_samples_2d()
+```
 
 ## License
-
 GNU Affero General Public License v3
 
 ## Citation
-
 If you use Masster in your research, please cite this repository.

masster-0.5.1/README.md

@@ -0,0 +1,101 @@
+# MASSter
+
+**MASSter** is a Python package for the analysis of mass spectrometry data, tailored for the purpose of metabolomics and LC-MS data processing. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. The sample-centric feature detection uses OpenMS. All other functionalities for e.g. centroiding, RT alignment, adduct and isotopomer detection, merging of multiple samples, gap-filling, quantification, etc. were redesigned and engineered to maximize scalability (tested with 3000 LC-MS), speed, quality, and results.
+
+This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. 
+
+## Prerequisites
+
+**MASSter** reads raw (Thermo), wiff (SCIEX), or mzML data. It's recommended to provide raw, profile data.
+
+## Installation
+
+```bash
+pip install masster
+```
+
+## Basic usage
+### Quick start: use the wizard
+
+```python
+import masster
+masster.wizard.execute(
+    source=r'..\..\folder_with_raw_data',
+    folder=r'..\..folder_to_store_results'
+    )
+```
+
+This will run a wizard that should perform all key steps and save the results to the `folder`.
+
+### Basic workflow for analyzing a single sample
+```python
+import masster
+sample = masster.Sample(filename='...') # full path to a *.raw, *.wiff, or *.mzML file
+# process
+sample.find_features(chrom_fwhm=0.5, noise=50) # for orbitrap data, set noise to 1e5
+sample.find_adducts()
+sample.find_ms2()
+
+# access data
+sample.features_df
+
+# save results
+sample.save() # stores to *.sample5, our custom hdf5 format
+sample.export_mgf()
+
+# some plots
+sample.plot_bpc()
+sample.plot_tic()
+sample.plot_2d()
+sample.plot_features_stats()
+
+# explore methods
+dir(study)
+```
+
+### Basic Workflow for analyzing LC-MS study with 2-... samples
+
+```python
+import masster
+# Initialize the Study object with the default folder
+study = masster.Study(folder=r'D:\...\mylcms')
+
+# Load data from folder with raw data, here: WIFF
+study.add(r'D:\...\...\...\*.wiff')
+
+# Perform retention time correction
+study.align(rt_tol=2.0)
+study.plot_alignment()
+study.plot_bpc()
+study.plot_rt_correction()
+
+# Find consensus features
+study.merge(min_samples=3)
+study.plot_consensus_2d()
+
+# Retrieve missing data for quantification
+study.fill()
+
+# Integrate according to consensus metadata
+study.integrate()
+
+# export results
+study.export_mgf()
+study.export_mztab()
+study.export_xlsx()
+study.export_parquet()
+
+# Save the study to .study5
+study.save()
+
+# Some of the plots...
+study.plot_samples_pca()
+study.plot_samples_umap()
+study.plot_samples_2d()
+```
+
+## License
+GNU Affero General Public License v3
+
+## Citation
+If you use Masster in your research, please cite this repository.

{masster-0.4.22 → masster-0.5.1}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.4.22"
+version = "0.5.1"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }
@@ -47,6 +47,8 @@ dependencies = [
     "openpyxl>=3.1.5",
     "cmap>=0.6.2",
     "scikit-learn>=1.7.1",
+    "umap-learn>=0.5.9.post2",
+    "hdbscan>=0.8.40",
 ]
 
 [project.optional-dependencies]

{masster-0.4.22 → masster-0.5.1}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.4.22"
+__version__ = "0.5.1"
 
 
 def get_version():

masster-0.5.1/src/masster/data/libs/aa.csv

@@ -0,0 +1,22 @@
+name,smiles,inchikey,formula,db_id,db
+L-Glutamic acid,N[C@@H](CCC(O)=O)C(O)=O,WHUUTDBJXJRKMK-VKHMYHEASA-N,C5H9NO4,CID:33032,pubchem
+L-Tyrosine,N[C@@H](CC1=CC=C(O)C=C1)C(O)=O,OUYCCCASQSFEME-QMMMGPOBSA-N,C9H11NO3,CID:6057,pubchem
+L-Phenylalanine,N[C@@H](CC1=CC=CC=C1)C(O)=O,COLNVLDHVKWLRT-QMMMGPOBSA-N,C9H11NO2,CID:6140,pubchem
+L-Alanine,C[C@H](N)C(O)=O,QNAYBMKLOCPYGJ-REOHCLBHSA-N,C3H7NO2,CID:5950,pubchem
+L-Proline,OC(=O)[C@@H]1CCCN1,ONIBWKKTOPOVIA-BYPYZUCNSA-N,C5H9NO2,CID:145742,pubchem
+L-Threonine,C[C@@H](O)[C@H](N)C(O)=O,AYFVYJQAPQTCCC-GBXIJSLDSA-N,C4H9NO3,CID:6288,pubchem
+L-Asparagine,N[C@@H](CC(N)=O)C(O)=O,DCXYFEDJOCDNAF-REOHCLBHSA-N,C4H8N2O3,CID:6267,pubchem
+L-Isoleucine,CC[C@H](C)[C@H](N)C(O)=O,AGPKZVBTJJNPAG-WHFBIAKZSA-N,C6H13NO2,CID:6306,pubchem
+L-Histidine,N[C@@H](CC1=CN=CN1)C(O)=O,HNDVDQJCIGZPNO-YFKPBYRVSA-N,C6H9N3O2,CID:6274,pubchem
+L-Lysine,NCCCC[C@H](N)C(O)=O,KDXKERNSBIXSRK-YFKPBYRVSA-N,C6H14N2O2,CID:5962,pubchem
+L-Serine,N[C@@H](CO)C(O)=O,MTCFGRXMJLQNBG-REOHCLBHSA-N,C3H7NO3,CID:5951,pubchem
+L-Aspartic acid,N[C@@H](CC(O)=O)C(O)=O,CKLJMWTZIZZHCS-REOHCLBHSA-N,C4H7NO4,CID:5960,pubchem
+L-Cystine,N[C@@H](CSSC[C@H](N)C(O)=O)C(O)=O,LEVWYRKDKASIDU-IMJSIDKUSA-N,C6H12N2O4S2,CID:67678,pubchem
+L-Arginine,N[C@@H](CCCNC(N)=N)C(O)=O,ODKSFYDXXFIFQN-BYPYZUCNSA-N,C6H14N4O2,CID:6322,pubchem
+L-Cysteine,N[C@@H](CS)C(O)=O,XUJNEKJLAYXESH-REOHCLBHSA-N,C3H7NO2S,CID:5862,pubchem
+L-Glutamine,N[C@@H](CCC(N)=O)C(O)=O,ZDXPYRJPNDTMRX-VKHMYHEASA-N,C5H10N2O3,CID:5961,pubchem
+L-Leucine,CC(C)C[C@H](N)C(O)=O,ROHFNLRQFUQHCH-YFKPBYRVSA-N,C6H13NO2,CID:6106,pubchem
+L-Methionine,CSCC[C@H](N)C(O)=O,FFEARJCKVFRZRR-BYPYZUCNSA-N,C5H11NO2S,CID:6137,pubchem
+L-Valine,CC(C)[C@H](N)C(O)=O,KZSNJWFQEVHDMF-BYPYZUCNSA-N,C5H11NO2,CID:6287,pubchem
+L-Tryptophan,N[C@@H](CC1=CNC2=C1C=CC=C2)C(O)=O,QIVBCDIJIAJPQS-VIFPVBQESA-N,C11H12N2O2,CID:6305,pubchem
+Glycine,NCC(O)=O,QNAYBMKLOCPYGJ-UHFFFAOYSA-N,C2H5NO2,CID:750,Glycine

{masster-0.4.22 → masster-0.5.1}/src/masster/lib/lib.py

@@ -123,11 +123,13 @@ class Lib:
             "inchi": pl.Series([], dtype=pl.Utf8),
             "inchikey": pl.Series([], dtype=pl.Utf8),
             "formula": pl.Series([], dtype=pl.Utf8),
+            "iso": pl.Series([], dtype=pl.Int64),
             "adduct": pl.Series([], dtype=pl.Utf8),
             "m": pl.Series([], dtype=pl.Float64),
             "z": pl.Series([], dtype=pl.Int8),
             "mz": pl.Series([], dtype=pl.Float64),
             "rt": pl.Series([], dtype=pl.Float64),
+            "quant_group": pl.Series([], dtype=pl.Int64),
             "db_id": pl.Series([], dtype=pl.Utf8),
             "db": pl.Series([], dtype=pl.Utf8),
         })
@@ -245,11 +247,13 @@ class Lib:
                 "inchi": compound_data.get("inchi", ""),
                 "inchikey": compound_data.get("inchikey", ""),
                 "formula": compound_data["formula"],
+                "iso": 0,  # Default to zero
                 "adduct": adduct,
                 "m": adducted_mass,
                 "z": charge,
                 "mz": mz,
                 "rt": compound_data.get("rt", None),
+                "quant_group": counter,  # Use same as lib_uid for default
                 "db_id": compound_data.get("db_id", None),
                 "db": compound_data.get("db", None),
             }
@@ -526,12 +530,14 @@ class Lib:
                     "source_id": match_row.get("source_id"),
                     "name": match_row["name"],
                     "formula": match_row["formula"],
+                    "iso": match_row.get("iso", 0),
                     "adduct": match_row["adduct"],
                     "smiles": match_row["smiles"],
                     "inchi": match_row["inchi"],
                     "inchikey": match_row["inchikey"],
                     "lib_mz": match_row["mz"],
                     "lib_rt": match_row["rt"],
+                    "quant_group": match_row.get("quant_group"),
                     "delta_mz": abs(feature_mz - match_row["mz"]),
                     "delta_rt": abs(feature_rt - match_row["rt"]) if feature_rt is not None and match_row["rt"] is not None else None,
                 }

{masster-0.4.22 → masster-0.5.1}/src/masster/sample/adducts.py

@@ -809,5 +809,5 @@ def find_adducts(self, **kwargs):
         ["name", "charge", "mass_shift", "probability"],
     ).to_dicts()
 
-    self.store_history(["find_adducts"], history_params)
+    self.update_history(["find_adducts"], history_params)
     self.logger.debug("Parameters stored successfully")

{masster-0.4.22 → masster-0.5.1}/src/masster/sample/load.py

@@ -173,8 +173,8 @@ def load_noms1(
         self.label = label
 
 
-# Backward compatibility alias
-def load_study(
+# Renamed for clarity and internal use
+def _load_ms1(
     self,
     filename=None,
     ondisk=False,
@@ -182,7 +182,8 @@ def load_study(
     label=None,
 ):
     """
-    Backward compatibility alias for load_noms1().
+    Load MS1-only data (renamed from load_study for clarity).
+    Optimized version for study loading that excludes MS2 data.
 
     This method is deprecated. Use load_noms1() instead.
     """
@@ -828,11 +829,11 @@ def _load_mzpkl(
             continue
         if k == "spectra_df":
             k = "scans_df"
-        setattr(self, k, v)
+    setattr(self, k, v)
 
-    self.sanitize()
-
-    if self.ondisk:
+# Import and call internal sanitize function
+from masster.study.load import _sanitize
+_sanitize(self)    if self.ondisk:
         self.file_obj = oms.OnDiscMSExperiment()
     else:
         self.file_obj = oms.MSExperiment()
@@ -955,7 +956,7 @@ def sanitize(self):
                         self.features_df.at[_i, "ms2_specs"][_j] = new_ms2_specs
 
 
-def index_file(self):
+def _index_file(self):
     """
     Reload raw data from a file based on its extension.
 
@@ -1022,7 +1023,7 @@ def index_file(self):
             raise FileNotFoundError(
                 f"File {self.file_source} not found. Did the path change? Consider running source().",
             )
-        self.index_file()
+        self._index_file()
     else:
         raise FileNotFoundError(
             f"File {self.file_source} not found. Did the path change? Consider running source().",

{masster-0.4.22 → masster-0.5.1}/src/masster/sample/plot.py

@@ -1955,7 +1955,7 @@ def plot_dda_stats(
         return _display_plot(layout, layout_obj)
 
 
-def plot_feature_stats(
+def plot_features_stats(
     self,
     filename=None,
 ):

{masster-0.4.22 → masster-0.5.1}/src/masster/sample/processing.py

@@ -799,7 +799,7 @@ def find_features(self, **kwargs):
     self.logger.info(f"Feature detection completed. Total features: {len(df)}")
 
     # store params
-    self.store_history(["find_features"], params.to_dict())
+    self.update_history(["find_features"], params.to_dict())
     self.logger.debug(
         "Parameters stored to find_features",
     )
@@ -1114,7 +1114,7 @@ def find_ms2(self, **kwargs):
     c = 0
 
     if self.file_interface is None:
-        self.index_file()
+        self._index_file()
 
     # Vectorize the entire operation for better performance
     features_subset = features_df.filter(pl.col("feature_uid").is_in(feature_uid_list))
@@ -1269,7 +1269,7 @@ def find_ms2(self, **kwargs):
     self.features_df = features_df
 
     # store params
-    self.store_history(["find_ms2"], params.to_dict())
+    self.update_history(["find_ms2"], params.to_dict())
     self.logger.debug(
         "Parameters stored to find_ms2",
     )
@@ -1430,4 +1430,4 @@ def find_iso(self, rt_tolerance: float = 0.1, **kwargs):
     # Store parameters in history
     params_dict = {"rt_tolerance": rt_tolerance}
     params_dict.update(kwargs)
-    self.store_history(["find_iso"], params_dict)
+    self.update_history(["find_iso"], params_dict)

{masster-0.4.22 → masster-0.5.1}/src/masster/sample/sample.py

@@ -47,17 +47,17 @@ from masster.sample.defaults.find_adducts_def import find_adducts_defaults
 from masster.sample.defaults.find_ms2_def import find_ms2_defaults
 from masster.sample.defaults.get_spectrum_def import get_spectrum_defaults
 
-# Sample-specific imports
-from masster.sample.h5 import _load_sample5
-from masster.sample.h5 import _load_sample5_study
-from masster.sample.h5 import _save_sample5
-from masster.sample.helpers import _delete_ms2
+# Sample-specific imports - keeping these private, only for internal use
+# from masster.sample.h5 import _load_sample5
+# from masster.sample.h5 import _load_sample5_study
+# from masster.sample.h5 import _save_sample5
+# from masster.sample.helpers import _delete_ms2
 from masster.sample.helpers import _estimate_memory_usage
 from masster.sample.helpers import _get_scan_uids
 from masster.sample.helpers import _get_feature_uids
-from masster.sample.helpers import _features_sync
-from masster.sample.adducts import _get_adducts
+# from masster.sample.helpers import _features_sync - made internal only
 from masster.sample.adducts import find_adducts
+# Removed _get_adducts - only used in study modules
 from masster.sample.helpers import features_delete
 from masster.sample.helpers import features_filter
 from masster.sample.helpers import select
@@ -69,22 +69,23 @@ from masster.sample.helpers import get_eic
 from masster.sample.helpers import set_source
 from masster.sample.helpers import _recreate_feature_map
 from masster.sample.helpers import _get_feature_map
-from masster.sample.load import _load_featureXML
-from masster.sample.load import _load_ms2data
-from masster.sample.load import _load_mzML
-from masster.sample.load import _load_raw
-from masster.sample.load import _load_wiff
+# Load functions - keeping only specific ones needed for external API
+# from masster.sample.load import _load_featureXML - made internal only
+# from masster.sample.load import _load_ms2data - made internal only  
+# from masster.sample.load import _load_mzML - made internal only
+# from masster.sample.load import _load_raw - made internal only
+# from masster.sample.load import _load_wiff - made internal only
 from masster.sample.load import chrom_extract
-from masster.sample.load import index_file
+from masster.sample.load import _index_file
 from masster.sample.load import load
 from masster.sample.load import load_noms1
-from masster.sample.load import load_study
+from masster.sample.load import _load_ms1  # Renamed from load_study
 from masster.sample.load import sanitize
 from masster.sample.plot import plot_2d
 from masster.sample.plot import plot_2d_oracle
 from masster.sample.plot import plot_dda_stats
 from masster.sample.plot import plot_chrom
-from masster.sample.plot import plot_feature_stats
+from masster.sample.plot import plot_features_stats  # Renamed from plot_feature_stats
 from masster.sample.plot import plot_ms2_cycle
 from masster.sample.plot import plot_ms2_eic
 from masster.sample.plot import plot_ms2_q1
@@ -105,12 +106,12 @@ from masster.sample.parameters import get_parameters
 from masster.sample.parameters import update_parameters
 from masster.sample.parameters import get_parameters_property
 from masster.sample.parameters import set_parameters_property
-from masster.sample.save import _save_featureXML
 from masster.sample.save import export_chrom
 from masster.sample.save import export_dda_stats
 from masster.sample.save import export_features
 from masster.sample.save import export_mgf
 from masster.sample.save import save
+# Removed internal-only import: _save_featureXML
 
 
 class Sample:
@@ -215,7 +216,8 @@ class Sample:
     # Attach module functions as class methods
     load = load
     load_noms1 = load_noms1
-    load_study = load_study
+    _load_ms1 = _load_ms1  # Renamed from load_study for clarity
+    load_study = _load_ms1  # Backward compatibility alias
     save = save
     find_features = find_features
     find_adducts = find_adducts
@@ -230,6 +232,7 @@ class Sample:
     select_features = select
     analyze_dda = analyze_dda
     store_history = store_history
+    update_history = store_history  # Preferred name for consistency with Study class
     get_parameters = get_parameters
     update_parameters = update_parameters
     get_parameters_property = get_parameters_property
@@ -242,7 +245,8 @@ class Sample:
     plot_2d_oracle = plot_2d_oracle
     plot_dda_stats = plot_dda_stats
     plot_chrom = plot_chrom
-    plot_feature_stats = plot_feature_stats
+    plot_features_stats = plot_features_stats  # Renamed from plot_feature_stats
+    plot_feature_stats = plot_features_stats  # Backward compatibility alias
     plot_ms2_cycle = plot_ms2_cycle
     plot_ms2_eic = plot_ms2_eic
     plot_ms2_q1 = plot_ms2_q1
@@ -259,30 +263,21 @@ class Sample:
     _get_feature_map = _get_feature_map
 
     # Additional method assignments for all imported functions
-    _load_sample5 = _load_sample5
-    _load_sample5_study = _load_sample5_study
-    _save_sample5 = _save_sample5
-    _delete_ms2 = _delete_ms2
+    # Removed internal-only methods: _load_sample5, _load_sample5_study, _save_sample5, _delete_ms2, _features_sync
     _estimate_memory_usage = _estimate_memory_usage
     _get_scan_uids = _get_scan_uids
     _get_feature_uids = _get_feature_uids
-    _features_sync = _features_sync
     features_delete = features_delete
     features_filter = features_filter
-    _load_featureXML = _load_featureXML
-    _load_ms2data = _load_ms2data
-    _load_mzML = _load_mzML
-    _load_raw = _load_raw
-    _load_wiff = _load_wiff
+    # Removed internal-only load methods: _load_featureXML, _load_ms2data, _load_mzML, _load_raw, _load_wiff
     chrom_extract = chrom_extract
-    index_file = index_file
+    _index_file = _index_file  # Renamed from index_file to be internal-only
     sanitize = sanitize
     _clean_features_df = _clean_features_df
     _features_deisotope = _features_deisotope
     _get_ztscan_stats = _get_ztscan_stats
     _spec_to_mat = _spec_to_mat
-    _save_featureXML = _save_featureXML
-    _get_adducts = _get_adducts
+    # Removed internal-only methods: _save_featureXML, _get_adducts (used only in study modules)
 
     # defaults
     sample_defaults = sample_defaults
@@ -303,12 +298,14 @@ class Sample:
         """
         # Define backward compatibility aliases to hide
         backward_compatibility_aliases = {
-            'load_study',           # deprecated alias for load_noms1
+            'load_study',           # deprecated alias for _load_ms1
             'filter_features',      # alias for filter (deprecated naming)
             'select_features',      # alias for select (deprecated naming)
             'features_filter',      # confusing duplicate of filter
             'features_select',      # confusing duplicate of select
             'merge_defaults',       # alias for find_features_defaults (confusing)
+            'plot_feature_stats',   # backward compatibility for plot_features_stats
+            'store_history',        # deprecated alias for update_history
         }
         
         # Get all attributes from the class