masster 0.5.28__tar.gz → 0.6.0__tar.gz

{masster-0.5.28 → masster-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.28
+Version: 0.6.0
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -734,19 +734,19 @@ Description-Content-Type: text/markdown
 
 ## Background and motivation
 
-MASSter is actively used, maintainted, and developed by the Zamboni Lab at ETH Zurich. The project started because many needs of were unmatched by the "usual" software packages (mzmine, msdial, W4M, ...), e.g. performance, scalability, sensitivity, robustness, speed, rapid implementation of new features, embedding in ETL systems, and so on. 
+MASSter is actively used, maintained, and developed by the Zamboni Lab at ETH Zurich. The project started because many needs were unmet by the "usual" software packages (mzMine, MS-DIAL, Workflow4Metabolomics (W4M), ...), for example performance, scalability, sensitivity, robustness, speed, rapid implementation of new features, and embedding in ETL systems.
 
-All methods include a long list of parameters, and might wrap alternative algorithms. These are only relevant for advanced users. We recommend running the processing methods with defaults, or using the Wizard.  
+All methods include many parameters and may wrap alternative algorithms. These options are primarily relevant for advanced users. We recommend running the processing methods with the defaults or using the Wizard.
 
 ## Content
 
 MASSter is designed to deal with DDA data, and hides functionalities for DIA and ZTScan DIA data. The sample-centric feature detection uses OpenMS, which is both accurate and fast, and it was wrapped with additional code to improve isotope and adduct detection. All other functionalities are own implementations: centroiding, RT alignment, adduct and isotopomer detection, merging of multiple samples, gap-filling, quantification, etc. 
 
-MASSter was engineered to maximize quality of results, sensitivity, scalability, and also speed. Yes, it's Python which is notoriously slower than other languages, but considerable time was spent in speeding up everything, including the systematic use of [polars](https://pola.rs/), numpy vectorization, multiprocessing, chunking, etc. MASSter was tested with studies with 3000+ LC-MS/MS samples (1 Mio MS2 spectra), and it autonomously completed analysis within a few hours. 
+MASSter was engineered to maximize result quality, sensitivity, scalability, and speed. Yes, it's Python, which can be slower than other languages, but considerable effort was spent on optimizations, including the systematic use of [Polars](https://pola.rs/), NumPy vectorization, multiprocessing, and chunking. MASSter has been tested on studies with 3,000+ LC–MS/MS samples (≈1 million MS2 spectra) and autonomously completed analyses within a few hours.
 
 ## Architecture
 
-MASSter defines own classes for Spectra, Chromatograms, Libraries, Samples, and Studies (= bunch of samples, i.e. a LC-MS sequence). Users will deal mostly with one Study() object at the time. Sample() objects are created when analyzing a batch - and saved for caching -, or will be used only for development, troubleshooting, or to generate illustrations. 
+MASSter defines classes for Spectra, Chromatograms, Libraries, Samples, and Studies (a Study is a collection of samples, i.e. an LC–MS sequence). Users will typically work with a single `Study` object at a time. `Sample` objects are created when analyzing a batch (and saved for caching), or used for development, troubleshooting, or generating illustrations.
 
 The analysis can be done in scripts (without user intervention, e.g. by the integrated Wizard), or interactively in notebooks, i.e. [marimo](https://marimo.io/) or [jupyter](https://jupyter.org/).
 
@@ -756,9 +756,9 @@ You'll need to install Python (3.10-3.13, 3.14 has not been tested yet).
 
 MASSter reads raw (Thermo), wiff (SCIEX), or mzML data. Reading vendor formats relies on .NET libraries, and is only possible in Windows. On Linux or MacOS, you'll be forced to use mzML data.
 
-**It's recommended to use data in either vendor's raw format (wiff and raw) or mzML in profile data.** MASSter includes a sophisticated and sufficiently fast centroiding algorithm that works well across the full dynamic range and will only act on the spectra that are relevant. In our tests with data from different vendors, the centroiding performed much better than most Vendor's implementations (that are primarily proteomics-centric). 
+**It's recommended to use data in either the vendor's raw formats (WIFF and Thermo RAW) or mzML in profile mode.** MASSter includes a sophisticated and sufficiently fast centroiding algorithm that works well across the full dynamic range and will only act on spectra that are relevant. In our tests with data from different vendors, the centroiding performed much better than most vendor implementations (which are primarily proteomics-centric).
 
-If still want to convert raw data to centroided mzML, please use (CentroidR)[https://github.com/Adafede/CentroidR/tree/0.0.0.9001]. 
+If you still want to convert raw data to centroided mzML, please use CentroidR: https://github.com/Adafede/CentroidR/tree/0.0.0.9001
 
 ## Installation
 
@@ -769,7 +769,7 @@ pip install masster
 ## Getting started
 **The quickest way to use, or learn how to use MASSter, is to use the Wizard** which we integrated and, ideally, takes care of everything automatically. 
 
-The Wizard only needs to know where to find the MS files and were the store the results.
+The Wizard only needs to know where to find the MS files and where to store the results.
 ```python
 from masster import Wizard
 wiz = Wizard(
@@ -780,15 +780,15 @@ wiz = Wizard(
 wiz.test_and_run()
 ```
 
-This will trigger the analysis of raw data, and the creation of a script to process all samples and then assemble the study. The whole processing will be stored as `1_masster_workflow.py` in the output folder. The wizard will test once and, if successull, run the full workflow using parallel processes. Once the processing is over you, navigate to `folder` to see what happened...
+This will trigger the analysis of raw data, and the creation of a script to process all samples and then assemble the study. The whole processing will be stored as `1_masster_workflow.py` in the output folder. The wizard will test once and, if successful, run the full workflow using parallel processes. Once the processing is over you, navigate to `folder` to see what happened...
 
 If you want to interact with your data, we recommend using [marimo](https://marimo.io/) or [jupyter](https://jupyter.org/) and open the `*.study5` file, for example:
 
 ```bash
-# use marimo to open the script created by marino
-marimo edit '..\..folder_to_store_results\2_interactive_analysis.py'
-# or, if you use uv to manage an environment with masster 
-uv run marimo edit '..\..folder_to_store_results\2_interactive_analysis.py'
+# use marimo to open the script created by marimo
+marimo edit '..\\..\\folder_to_store_results\\2_interactive_analysis.py'
+# or, if you use uv to manage an environment with masster
+uv run marimo edit '..\\..\\folder_to_store_results\\2_interactive_analysis.py'
 ```
 
 ### Basic Workflow for analyzing LC-MS study with 1-1000+ samples
@@ -874,7 +874,7 @@ sample.plot_2d()
 sample.plot_features_stats()
 
 # explore methods
-dir(study)
+dir(sample)
 ```
 
 ## Disclaimer
@@ -885,11 +885,9 @@ dir(study)
 - **Backward compatibility**: We do not guarantee backward compatibility between versions. Breaking changes may occur as we improve the software
 - **Performance**: While optimized for our workflows, performance may vary depending on your data and system configuration
 - **Results**: We do our best to ensure accuracy, but you should validate results independently for your research
-- **Support**: This is an academic project with limited resources. Community support is available through GitHub issues, but we cannot guarantee response times
+- **Support**: This is an academic project with limited resources. At the moment, we do not provide external user support.
 - **Production use**: If you plan to use MASSter in production or critical workflows, thorough testing with your data is recommended
 
-We welcome feedback, bug reports, and contributions via GitHub!
-
 ## License
 GNU Affero General Public License v3
 

{masster-0.5.28 → masster-0.6.0}/README.md

@@ -6,19 +6,19 @@
 
 ## Background and motivation
 
-MASSter is actively used, maintainted, and developed by the Zamboni Lab at ETH Zurich. The project started because many needs of were unmatched by the "usual" software packages (mzmine, msdial, W4M, ...), e.g. performance, scalability, sensitivity, robustness, speed, rapid implementation of new features, embedding in ETL systems, and so on. 
+MASSter is actively used, maintained, and developed by the Zamboni Lab at ETH Zurich. The project started because many needs were unmet by the "usual" software packages (mzMine, MS-DIAL, Workflow4Metabolomics (W4M), ...), for example performance, scalability, sensitivity, robustness, speed, rapid implementation of new features, and embedding in ETL systems.
 
-All methods include a long list of parameters, and might wrap alternative algorithms. These are only relevant for advanced users. We recommend running the processing methods with defaults, or using the Wizard.  
+All methods include many parameters and may wrap alternative algorithms. These options are primarily relevant for advanced users. We recommend running the processing methods with the defaults or using the Wizard.
 
 ## Content
 
 MASSter is designed to deal with DDA data, and hides functionalities for DIA and ZTScan DIA data. The sample-centric feature detection uses OpenMS, which is both accurate and fast, and it was wrapped with additional code to improve isotope and adduct detection. All other functionalities are own implementations: centroiding, RT alignment, adduct and isotopomer detection, merging of multiple samples, gap-filling, quantification, etc. 
 
-MASSter was engineered to maximize quality of results, sensitivity, scalability, and also speed. Yes, it's Python which is notoriously slower than other languages, but considerable time was spent in speeding up everything, including the systematic use of [polars](https://pola.rs/), numpy vectorization, multiprocessing, chunking, etc. MASSter was tested with studies with 3000+ LC-MS/MS samples (1 Mio MS2 spectra), and it autonomously completed analysis within a few hours. 
+MASSter was engineered to maximize result quality, sensitivity, scalability, and speed. Yes, it's Python, which can be slower than other languages, but considerable effort was spent on optimizations, including the systematic use of [Polars](https://pola.rs/), NumPy vectorization, multiprocessing, and chunking. MASSter has been tested on studies with 3,000+ LC–MS/MS samples (≈1 million MS2 spectra) and autonomously completed analyses within a few hours.
 
 ## Architecture
 
-MASSter defines own classes for Spectra, Chromatograms, Libraries, Samples, and Studies (= bunch of samples, i.e. a LC-MS sequence). Users will deal mostly with one Study() object at the time. Sample() objects are created when analyzing a batch - and saved for caching -, or will be used only for development, troubleshooting, or to generate illustrations. 
+MASSter defines classes for Spectra, Chromatograms, Libraries, Samples, and Studies (a Study is a collection of samples, i.e. an LC–MS sequence). Users will typically work with a single `Study` object at a time. `Sample` objects are created when analyzing a batch (and saved for caching), or used for development, troubleshooting, or generating illustrations.
 
 The analysis can be done in scripts (without user intervention, e.g. by the integrated Wizard), or interactively in notebooks, i.e. [marimo](https://marimo.io/) or [jupyter](https://jupyter.org/).
 
@@ -28,9 +28,9 @@ You'll need to install Python (3.10-3.13, 3.14 has not been tested yet).
 
 MASSter reads raw (Thermo), wiff (SCIEX), or mzML data. Reading vendor formats relies on .NET libraries, and is only possible in Windows. On Linux or MacOS, you'll be forced to use mzML data.
 
-**It's recommended to use data in either vendor's raw format (wiff and raw) or mzML in profile data.** MASSter includes a sophisticated and sufficiently fast centroiding algorithm that works well across the full dynamic range and will only act on the spectra that are relevant. In our tests with data from different vendors, the centroiding performed much better than most Vendor's implementations (that are primarily proteomics-centric). 
+**It's recommended to use data in either the vendor's raw formats (WIFF and Thermo RAW) or mzML in profile mode.** MASSter includes a sophisticated and sufficiently fast centroiding algorithm that works well across the full dynamic range and will only act on spectra that are relevant. In our tests with data from different vendors, the centroiding performed much better than most vendor implementations (which are primarily proteomics-centric).
 
-If still want to convert raw data to centroided mzML, please use (CentroidR)[https://github.com/Adafede/CentroidR/tree/0.0.0.9001]. 
+If you still want to convert raw data to centroided mzML, please use CentroidR: https://github.com/Adafede/CentroidR/tree/0.0.0.9001
 
 ## Installation
 
@@ -41,7 +41,7 @@ pip install masster
 ## Getting started
 **The quickest way to use, or learn how to use MASSter, is to use the Wizard** which we integrated and, ideally, takes care of everything automatically. 
 
-The Wizard only needs to know where to find the MS files and were the store the results.
+The Wizard only needs to know where to find the MS files and where to store the results.
 ```python
 from masster import Wizard
 wiz = Wizard(
@@ -52,15 +52,15 @@ wiz = Wizard(
 wiz.test_and_run()
 ```
 
-This will trigger the analysis of raw data, and the creation of a script to process all samples and then assemble the study. The whole processing will be stored as `1_masster_workflow.py` in the output folder. The wizard will test once and, if successull, run the full workflow using parallel processes. Once the processing is over you, navigate to `folder` to see what happened...
+This will trigger the analysis of raw data, and the creation of a script to process all samples and then assemble the study. The whole processing will be stored as `1_masster_workflow.py` in the output folder. The wizard will test once and, if successful, run the full workflow using parallel processes. Once the processing is over you, navigate to `folder` to see what happened...
 
 If you want to interact with your data, we recommend using [marimo](https://marimo.io/) or [jupyter](https://jupyter.org/) and open the `*.study5` file, for example:
 
 ```bash
-# use marimo to open the script created by marino
-marimo edit '..\..folder_to_store_results\2_interactive_analysis.py'
-# or, if you use uv to manage an environment with masster 
-uv run marimo edit '..\..folder_to_store_results\2_interactive_analysis.py'
+# use marimo to open the script created by marimo
+marimo edit '..\\..\\folder_to_store_results\\2_interactive_analysis.py'
+# or, if you use uv to manage an environment with masster
+uv run marimo edit '..\\..\\folder_to_store_results\\2_interactive_analysis.py'
 ```
 
 ### Basic Workflow for analyzing LC-MS study with 1-1000+ samples
@@ -146,7 +146,7 @@ sample.plot_2d()
 sample.plot_features_stats()
 
 # explore methods
-dir(study)
+dir(sample)
 ```
 
 ## Disclaimer
@@ -157,11 +157,9 @@ dir(study)
 - **Backward compatibility**: We do not guarantee backward compatibility between versions. Breaking changes may occur as we improve the software
 - **Performance**: While optimized for our workflows, performance may vary depending on your data and system configuration
 - **Results**: We do our best to ensure accuracy, but you should validate results independently for your research
-- **Support**: This is an academic project with limited resources. Community support is available through GitHub issues, but we cannot guarantee response times
+- **Support**: This is an academic project with limited resources. At the moment, we do not provide external user support.
 - **Production use**: If you plan to use MASSter in production or critical workflows, thorough testing with your data is recommended
 
-We welcome feedback, bug reports, and contributions via GitHub!
-
 ## License
 GNU Affero General Public License v3
 

{masster-0.5.28 → masster-0.6.0}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.5.28"
+version = "0.6.0"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.5.28 → masster-0.6.0}/src/masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.5.25"
+__version__ = "0.5.26"
 
 
 def get_version():

masster-0.6.0/src/masster/data/libs/aa_nort.json

@@ -0,0 +1,240 @@
+{
+  "version": "1.0",
+  "creation_date": "2025-10-30T14:38:00.595771",
+  "description": "Converted from CSV file aa.csv containing 21 records",
+  "source_file": "aa.csv",
+  "record_count": 21,
+  "data": [
+    {
+      "Name": "L-Glutamic acid",
+      "Formula": "C5H9NO4",
+      "SMILES": "N[C@@H](CCC(O)=O)C(O)=O",
+      "InChIKey": "WHUUTDBJXJRKMK-VKHMYHEASA-N",
+      "db_id": "CID:33032",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Tyrosine",
+      "Formula": "C9H11NO3",
+      "SMILES": "N[C@@H](CC1=CC=C(O)C=C1)C(O)=O",
+      "InChIKey": "OUYCCCASQSFEME-QMMMGPOBSA-N",
+      "db_id": "CID:6057",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Phenylalanine",
+      "Formula": "C9H11NO2",
+      "SMILES": "N[C@@H](CC1=CC=CC=C1)C(O)=O",
+      "InChIKey": "COLNVLDHVKWLRT-QMMMGPOBSA-N",
+      "db_id": "CID:6140",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Alanine",
+      "Formula": "C3H7NO2",
+      "SMILES": "C[C@H](N)C(O)=O",
+      "InChIKey": "QNAYBMKLOCPYGJ-REOHCLBHSA-N",
+      "db_id": "CID:5950",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Proline",
+      "Formula": "C5H9NO2",
+      "SMILES": "OC(=O)[C@@H]1CCCN1",
+      "InChIKey": "ONIBWKKTOPOVIA-BYPYZUCNSA-N",
+      "db_id": "CID:145742",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Threonine",
+      "Formula": "C4H9NO3",
+      "SMILES": "C[C@@H](O)[C@H](N)C(O)=O",
+      "InChIKey": "AYFVYJQAPQTCCC-GBXIJSLDSA-N",
+      "db_id": "CID:6288",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Asparagine",
+      "Formula": "C4H8N2O3",
+      "SMILES": "N[C@@H](CC(N)=O)C(O)=O",
+      "InChIKey": "DCXYFEDJOCDNAF-REOHCLBHSA-N",
+      "db_id": "CID:6267",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Isoleucine",
+      "Formula": "C6H13NO2",
+      "SMILES": "CC[C@H](C)[C@H](N)C(O)=O",
+      "InChIKey": "AGPKZVBTJJNPAG-WHFBIAKZSA-N",
+      "db_id": "CID:6306",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Histidine",
+      "Formula": "C6H9N3O2",
+      "SMILES": "N[C@@H](CC1=CN=CN1)C(O)=O",
+      "InChIKey": "HNDVDQJCIGZPNO-YFKPBYRVSA-N",
+      "db_id": "CID:6274",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Lysine",
+      "Formula": "C6H14N2O2",
+      "SMILES": "NCCCC[C@H](N)C(O)=O",
+      "InChIKey": "KDXKERNSBIXSRK-YFKPBYRVSA-N",
+      "db_id": "CID:5962",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Serine",
+      "Formula": "C3H7NO3",
+      "SMILES": "N[C@@H](CO)C(O)=O",
+      "InChIKey": "MTCFGRXMJLQNBG-REOHCLBHSA-N",
+      "db_id": "CID:5951",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Aspartic acid",
+      "Formula": "C4H7NO4",
+      "SMILES": "N[C@@H](CC(O)=O)C(O)=O",
+      "InChIKey": "CKLJMWTZIZZHCS-REOHCLBHSA-N",
+      "db_id": "CID:5960",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Cystine",
+      "Formula": "C6H12N2O4S2",
+      "SMILES": "N[C@@H](CSSC[C@H](N)C(O)=O)C(O)=O",
+      "InChIKey": "LEVWYRKDKASIDU-IMJSIDKUSA-N",
+      "db_id": "CID:67678",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Arginine",
+      "Formula": "C6H14N4O2",
+      "SMILES": "N[C@@H](CCCNC(N)=N)C(O)=O",
+      "InChIKey": "ODKSFYDXXFIFQN-BYPYZUCNSA-N",
+      "db_id": "CID:6322",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Cysteine",
+      "Formula": "C3H7NO2S",
+      "SMILES": "N[C@@H](CS)C(O)=O",
+      "InChIKey": "XUJNEKJLAYXESH-REOHCLBHSA-N",
+      "db_id": "CID:5862",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Glutamine",
+      "Formula": "C5H10N2O3",
+      "SMILES": "N[C@@H](CCC(N)=O)C(O)=O",
+      "InChIKey": "ZDXPYRJPNDTMRX-VKHMYHEASA-N",
+      "db_id": "CID:5961",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Leucine",
+      "Formula": "C6H13NO2",
+      "SMILES": "CC(C)C[C@H](N)C(O)=O",
+      "InChIKey": "ROHFNLRQFUQHCH-YFKPBYRVSA-N",
+      "db_id": "CID:6106",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Methionine",
+      "Formula": "C5H11NO2S",
+      "SMILES": "CSCC[C@H](N)C(O)=O",
+      "InChIKey": "FFEARJCKVFRZRR-BYPYZUCNSA-N",
+      "db_id": "CID:6137",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Valine",
+      "Formula": "C5H11NO2",
+      "SMILES": "CC(C)[C@H](N)C(O)=O",
+      "InChIKey": "KZSNJWFQEVHDMF-BYPYZUCNSA-N",
+      "db_id": "CID:6287",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "L-Tryptophan",
+      "Formula": "C11H12N2O2",
+      "SMILES": "N[C@@H](CC1=CNC2=C1C=CC=C2)C(O)=O",
+      "InChIKey": "QIVBCDIJIAJPQS-VIFPVBQESA-N",
+      "db_id": "CID:6305",
+      "db": "pubchem",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    },
+    {
+      "Name": "Glycine",
+      "Formula": "C2H5NO2",
+      "SMILES": "NCC(O)=O",
+      "InChIKey": "QNAYBMKLOCPYGJ-UHFFFAOYSA-N",
+      "db_id": "CID:750",
+      "db": "Glycine",
+      "rt": "",
+      "rt_min": "",
+      "rt_max": ""
+    }
+  ]
+}