From 8f6fecec71b5687cdfb7192b52d756350412b397 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Tue, 19 Nov 2024 19:12:26 +0100 Subject: [PATCH 01/11] Collect all Casanovo references on a dedicated citation page --- README.md | 15 +++++++++------ casanovo/casanovo.py | 20 ++++++++++++-------- docs/cite.md | 35 +++++++++++++++++++++++++++++++++++ docs/index.md | 12 +++++++++--- 4 files changed, 65 insertions(+), 17 deletions(-) create mode 100644 docs/cite.md diff --git a/README.md b/README.md index 35b7c646..ec12d0a3 100644 --- a/README.md +++ b/README.md @@ -4,13 +4,16 @@ ![image](https://user-images.githubusercontent.com/32707537/152622912-ca87da20-a64c-4e3f-9ca1-721c6b0d9c64.png) -If you use Casanovo in your work, please cite the following publications: +Casanovo is a state-of-the-art deep learning tool designed for _de novo_ peptide sequencing. +Powered by a transformer neural network, Casanovo "translates" peaks in MS/MS spectra into amino acid sequences with remarkable precision. +Achieving state-of-the-art performance, Casanovo is a versatile and powerful tool for discovery, with impactful applications in bottom-up proteomics, immunopeptidomics, metaproteomics, and beyond. -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) +Why choose Casanovo? -## Documentation - -#### https://casanovo.readthedocs.io/en/latest/ +- Unmatched accuracy: Cutting-edge AI ensures precise and reliable peptide sequencing, even in challenging datasets. +- Open-source innovation: Freely available and easy to integrate into existing visualization workflows. +- Actively maintained: Join a growing network of researchers and developers to stay at the forefront of technology. +## [Documentation](https://casanovo.readthedocs.io/en/latest/) +## [Citation information](https://casanovo.readthedocs.io/en/latest/cite.html) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 8bdfa58f..f0e0d2f2 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -95,20 +95,24 @@ def __init__(self, *args, **kwargs) -> None: def main() -> None: """# Casanovo - Casanovo de novo sequences peptides from tandem mass spectra using a - Transformer model. Casanovo currently supports mzML, mzXML, and MGF files - for de novo sequencing and annotated MGF files, such as those from - MassIVE-KB, for training new models. + Casanovo is a state-of-the-art deep learning tool designed for de + novo peptide sequencing. Powered by a transformer neural network, + Casanovo "translates" peaks in MS/MS spectra into amino acid + sequences. Links: - Documentation: [https://casanovo.readthedocs.io]() - Official code repository: [https://github.com/Noble-Lab/casanovo]() If you use Casanovo in your work, please cite: - - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo - mass spectrometry peptide sequencing with a transformer model. Proceedings - of the 39th International Conference on Machine Learning - ICML '22 (2022) - doi:10.1101/2022.02.07.479481. + - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., + Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence + translation from mass spectra to peptides with a transformer model. + in Nature Communications 15, 6427 (2024). + doi:10.1038/s41467-024-49731-x + + For more information on how to cite different versions of Casanovo, + please see [https://casanovo.readthedocs.io/en/latest/cite.html](). """ return diff --git a/docs/cite.md b/docs/cite.md new file mode 100644 index 00000000..6b92bab8 --- /dev/null +++ b/docs/cite.md @@ -0,0 +1,35 @@ +# How to Cite Casanovo + +When using Casanovo in your research, please cite the relevant scientific publications to acknowledge the work and contributions behind the tool. +Below, you will find detailed information on how to cite Casanovo, including citations for its various versions and functionalities. + +### Main Reference: Casanovo v4.x + +For general use of Casanovo, please cite the following paper: + +Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) + +### Casanovo v2.x: Spectrum Transformer Neural Network + +For research involving the spectrum transformer neural network architecture introduced in Casanovo v2.x: + +Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) + +### Casanovo v4.2.x: Accounting for Digestion Enzyme Bias + +For work involving Casanovo's enhanced performance on tryptic and non-tryptic data: + +Melendez, C., Sanders, J., Yilmaz, M., Bittremieux, W., Fondrie, W. E., Oh, S. & Noble, W. S. Accounting for digestion enzyme bias in Casanovo. in *Journal of Proteome Research* **23**, 4761–4769 (2024). [doi:10.1021/acs.jproteome.4c00422](https://doi.org/10.1021/acs.jproteome.4c00422) + +### Casanovo for Database Searching + +For using Casanovo as a learned score function for sequence database searching: + +Ananth, V., Sanders, J., Yilmaz, M., Wen, B., Oh, S. & Noble, W. S. A learned score function improves the power of mass spectrometry database search. in *Bioinformatics* **40**, i410–i417 (2024). [doi:10.1093/bioinformatics/btae218](https://doi.org/10.1093/bioinformatics/btae218) + +## Notes for Citation + +- Always ensure you are citing the correct version or functionality of Casanovo relevant to your use case. +- If you have questions about how to cite Casanovo in specific scenarios, feel free to reach out to the Casanovo community or maintainers. + +By citing Casanovo appropriately, you help support the ongoing development and innovation of this open-source tool. Thank you for contributing to the community! diff --git a/docs/index.md b/docs/index.md index 3dd77622..1d202e69 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,10 +4,15 @@ ![image](https://user-images.githubusercontent.com/32707537/152622912-ca87da20-a64c-4e3f-9ca1-721c6b0d9c64.png) -If you use Casanovo in your work, please cite the following publications: +Casanovo is a state-of-the-art deep learning tool designed for _de novo_ peptide sequencing. +Powered by a transformer neural network, Casanovo "translates" peaks in MS/MS spectra into amino acid sequences with remarkable precision. +Achieving state-of-the-art performance, Casanovo is a versatile and powerful tool for discovery, with impactful applications in bottom-up proteomics, immunopeptidomics, metaproteomics, and beyond. -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) -- Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) +Why choose Casanovo? + +- Unmatched accuracy: Cutting-edge AI ensures precise and reliable peptide sequencing, even in challenging datasets. +- Open-source innovation: Freely available and easy to integrate into existing visualization workflows. +- Actively maintained: Join a growing network of researchers and developers to stay at the forefront of technology. ```{toctree} --- @@ -17,6 +22,7 @@ maxdepth: 1 Getting Started File Formats FAQs +Citing Contributing Code of Conduct Changelog From cd82db3895d701069f4100fb6b13d37bcbdcfdc8 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 19 Nov 2024 18:17:26 +0000 Subject: [PATCH 02/11] Generate new screengrabs with rich-codex --- docs/images/help.svg | 178 ++++++++++++++++++++++--------------------- 1 file changed, 93 insertions(+), 85 deletions(-) diff --git a/docs/images/help.svg b/docs/images/help.svg index eae8e93d..05796ab6 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + - + - + - - $ casanovo --help - -Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     - - ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  - ┃                                  Casanovo                                  ┃  - ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  - Casanovo de novo sequences peptides from tandem mass spectra using a            - Transformer model. Casanovo currently supports mzML, mzXML, and MGF files for   - de novo sequencing and annotated MGF files, such as those from MassIVE-KB, for  - training new models.                                                            - - Links:                                                                          - - • Documentation: https://casanovo.readthedocs.io - • Official code repository: https://github.com/Noble-Lab/casanovo - - If you use Casanovo in your work, please cite:                                  - - • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   -mass spectrometry peptide sequencing with a transformer model. Proceedings   -of the 39th International Conference on Machine Learning - ICML '22 (2022)   -doi:10.1101/2022.02.07.479481.                                               - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--help-h    Show this message and exit.                                    │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────╮ -│configure Generate a Casanovo configuration file to customize.              │ -│evaluate  Evaluate de novo peptide sequencing performance.                  │ -│sequence  De novo sequence peptides from tandem mass spectra.               │ -│train     Train a Casanovo model on your own data.                          │ -│version   Get the Casanovo version information                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo is a state-of-the-art deep learning tool designed for de novo peptide  + sequencing. Powered by a transformer neural network, Casanovo "translates"      + peaks in MS/MS spectra into amino acid sequences.                               + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io + • Official code repository: https://github.com/Noble-Lab/casanovo + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R.,     +Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from      +mass spectra to peptides with a transformer model. in Nature Communications  +15, 6427 (2024). doi:10.1038/s41467-024-49731-x                              + + For more information on how to cite different versions of Casanovo, please see  +https://casanovo.readthedocs.io/en/latest/cite.html.                            + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│evaluate  Evaluate de novo peptide sequencing performance.                  │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 2f4753046207634f253a21bf296a100f27b6d1f5 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Thu, 21 Nov 2024 17:30:18 +0100 Subject: [PATCH 03/11] Update citation information --- README.md | 2 +- casanovo/casanovo.py | 9 ++++----- docs/cite.md | 22 +++++++--------------- docs/index.md | 2 +- 4 files changed, 13 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index ec12d0a3..6e5f2643 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ Casanovo is a state-of-the-art deep learning tool designed for _de novo_ peptide sequencing. Powered by a transformer neural network, Casanovo "translates" peaks in MS/MS spectra into amino acid sequences with remarkable precision. -Achieving state-of-the-art performance, Casanovo is a versatile and powerful tool for discovery, with impactful applications in bottom-up proteomics, immunopeptidomics, metaproteomics, and beyond. +Casanovo can be used for to find unexpected peptide sequences in any data-dependent acquisition, bottom-up tandem mass spectrometry dataset, and is particularly useful for immunopeptidomics, metaproteomics, paleoproteomics, venomics, or any setting in which you are interested in identifying peptides that may not be in your protein database. Why choose Casanovo? diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index f0e0d2f2..83d21e2e 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -105,11 +105,10 @@ def main() -> None: - Official code repository: [https://github.com/Noble-Lab/casanovo]() If you use Casanovo in your work, please cite: - - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., - Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence - translation from mass spectra to peptides with a transformer model. - in Nature Communications 15, 6427 (2024). - doi:10.1038/s41467-024-49731-x + - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. + De novo mass spectrometry peptide sequencing with a transformer + model. Proceedings of the 39th International Conference on Machine + Learning - ICML '22 (2022). doi:10.1101/2022.02.07.479481. For more information on how to cite different versions of Casanovo, please see [https://casanovo.readthedocs.io/en/latest/cite.html](). diff --git a/docs/cite.md b/docs/cite.md index 6b92bab8..fd67a481 100644 --- a/docs/cite.md +++ b/docs/cite.md @@ -3,28 +3,19 @@ When using Casanovo in your research, please cite the relevant scientific publications to acknowledge the work and contributions behind the tool. Below, you will find detailed information on how to cite Casanovo, including citations for its various versions and functionalities. -### Main Reference: Casanovo v4.x - For general use of Casanovo, please cite the following paper: -Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) - -### Casanovo v2.x: Spectrum Transformer Neural Network - -For research involving the spectrum transformer neural network architecture introduced in Casanovo v2.x: - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mass spectrometry peptide sequencing with a transformer model. in *Proceedings of the 39th International Conference on Machine Learning - ICML '22* vol. 162 25514–25522 (PMLR, 2022). [https://proceedings.mlr.press/v162/yilmaz22a.html](https://proceedings.mlr.press/v162/yilmaz22a.html) -### Casanovo v4.2.x: Accounting for Digestion Enzyme Bias +In addition, you may wish to cite one or more of these additional publications, depending on relevance to your work. -For work involving Casanovo's enhanced performance on tryptic and non-tryptic data: +- For improved performance of Casanovo by training on the MassIVE-KB data and applications in immunopeptidomics, metaproteomics, and the dark human proteome (Casanovo v4.x): +Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) +- For work involving Casanovo's enhanced performance on tryptic and non-tryptic data (Casanovo v4.2.x): Melendez, C., Sanders, J., Yilmaz, M., Bittremieux, W., Fondrie, W. E., Oh, S. & Noble, W. S. Accounting for digestion enzyme bias in Casanovo. in *Journal of Proteome Research* **23**, 4761–4769 (2024). [doi:10.1021/acs.jproteome.4c00422](https://doi.org/10.1021/acs.jproteome.4c00422) -### Casanovo for Database Searching - -For using Casanovo as a learned score function for sequence database searching: - +- For using Casanovo as a learned score function for sequence database searching (Casanovo-DB): Ananth, V., Sanders, J., Yilmaz, M., Wen, B., Oh, S. & Noble, W. S. A learned score function improves the power of mass spectrometry database search. in *Bioinformatics* **40**, i410–i417 (2024). [doi:10.1093/bioinformatics/btae218](https://doi.org/10.1093/bioinformatics/btae218) ## Notes for Citation @@ -32,4 +23,5 @@ Ananth, V., Sanders, J., Yilmaz, M., Wen, B., Oh, S. & Noble, W. S. A learned sc - Always ensure you are citing the correct version or functionality of Casanovo relevant to your use case. - If you have questions about how to cite Casanovo in specific scenarios, feel free to reach out to the Casanovo community or maintainers. -By citing Casanovo appropriately, you help support the ongoing development and innovation of this open-source tool. Thank you for contributing to the community! +By citing Casanovo appropriately, you help support the ongoing development and innovation of this open-source tool. +Thank you for contributing to the community. diff --git a/docs/index.md b/docs/index.md index 1d202e69..44312839 100644 --- a/docs/index.md +++ b/docs/index.md @@ -6,7 +6,7 @@ Casanovo is a state-of-the-art deep learning tool designed for _de novo_ peptide sequencing. Powered by a transformer neural network, Casanovo "translates" peaks in MS/MS spectra into amino acid sequences with remarkable precision. -Achieving state-of-the-art performance, Casanovo is a versatile and powerful tool for discovery, with impactful applications in bottom-up proteomics, immunopeptidomics, metaproteomics, and beyond. +Casanovo can be used for to find unexpected peptide sequences in any data-dependent acquisition, bottom-up tandem mass spectrometry dataset, and is particularly useful for immunopeptidomics, metaproteomics, paleoproteomics, venomics, or any setting in which you are interested in identifying peptides that may not be in your protein database. Why choose Casanovo? From a05560784c08bbc4aab5b92e484619f9b6cb090c Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Thu, 21 Nov 2024 17:33:01 +0100 Subject: [PATCH 04/11] Newlines in list --- docs/cite.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/cite.md b/docs/cite.md index fd67a481..31110ad9 100644 --- a/docs/cite.md +++ b/docs/cite.md @@ -10,12 +10,15 @@ Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mas In addition, you may wish to cite one or more of these additional publications, depending on relevance to your work. - For improved performance of Casanovo by training on the MassIVE-KB data and applications in immunopeptidomics, metaproteomics, and the dark human proteome (Casanovo v4.x): + Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) - For work involving Casanovo's enhanced performance on tryptic and non-tryptic data (Casanovo v4.2.x): + Melendez, C., Sanders, J., Yilmaz, M., Bittremieux, W., Fondrie, W. E., Oh, S. & Noble, W. S. Accounting for digestion enzyme bias in Casanovo. in *Journal of Proteome Research* **23**, 4761–4769 (2024). [doi:10.1021/acs.jproteome.4c00422](https://doi.org/10.1021/acs.jproteome.4c00422) - For using Casanovo as a learned score function for sequence database searching (Casanovo-DB): + Ananth, V., Sanders, J., Yilmaz, M., Wen, B., Oh, S. & Noble, W. S. A learned score function improves the power of mass spectrometry database search. in *Bioinformatics* **40**, i410–i417 (2024). [doi:10.1093/bioinformatics/btae218](https://doi.org/10.1093/bioinformatics/btae218) ## Notes for Citation From 5ec7ef1b384e76a5d5017abfc92a4ae7a30e8148 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Thu, 21 Nov 2024 17:33:27 +0100 Subject: [PATCH 05/11] Attempt 2 --- docs/cite.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/cite.md b/docs/cite.md index 31110ad9..88853d84 100644 --- a/docs/cite.md +++ b/docs/cite.md @@ -10,15 +10,15 @@ Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mas In addition, you may wish to cite one or more of these additional publications, depending on relevance to your work. - For improved performance of Casanovo by training on the MassIVE-KB data and applications in immunopeptidomics, metaproteomics, and the dark human proteome (Casanovo v4.x): - + Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) - For work involving Casanovo's enhanced performance on tryptic and non-tryptic data (Casanovo v4.2.x): - + Melendez, C., Sanders, J., Yilmaz, M., Bittremieux, W., Fondrie, W. E., Oh, S. & Noble, W. S. Accounting for digestion enzyme bias in Casanovo. in *Journal of Proteome Research* **23**, 4761–4769 (2024). [doi:10.1021/acs.jproteome.4c00422](https://doi.org/10.1021/acs.jproteome.4c00422) - For using Casanovo as a learned score function for sequence database searching (Casanovo-DB): - + Ananth, V., Sanders, J., Yilmaz, M., Wen, B., Oh, S. & Noble, W. S. A learned score function improves the power of mass spectrometry database search. in *Bioinformatics* **40**, i410–i417 (2024). [doi:10.1093/bioinformatics/btae218](https://doi.org/10.1093/bioinformatics/btae218) ## Notes for Citation From fc3eeac44d059dfef6534e9529d956278730a762 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Thu, 21 Nov 2024 17:33:56 +0100 Subject: [PATCH 06/11] Nevermind --- docs/cite.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/docs/cite.md b/docs/cite.md index 88853d84..fd67a481 100644 --- a/docs/cite.md +++ b/docs/cite.md @@ -10,15 +10,12 @@ Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. *De novo* mas In addition, you may wish to cite one or more of these additional publications, depending on relevance to your work. - For improved performance of Casanovo by training on the MassIVE-KB data and applications in immunopeptidomics, metaproteomics, and the dark human proteome (Casanovo v4.x): - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R., Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from mass spectra to peptides with a transformer model. in *Nature Communications* **15**, 6427 (2024). [doi:10.1038/s41467-024-49731-x](https://doi.org/10.1038/s41467-024-49731-x) - For work involving Casanovo's enhanced performance on tryptic and non-tryptic data (Casanovo v4.2.x): - Melendez, C., Sanders, J., Yilmaz, M., Bittremieux, W., Fondrie, W. E., Oh, S. & Noble, W. S. Accounting for digestion enzyme bias in Casanovo. in *Journal of Proteome Research* **23**, 4761–4769 (2024). [doi:10.1021/acs.jproteome.4c00422](https://doi.org/10.1021/acs.jproteome.4c00422) - For using Casanovo as a learned score function for sequence database searching (Casanovo-DB): - Ananth, V., Sanders, J., Yilmaz, M., Wen, B., Oh, S. & Noble, W. S. A learned score function improves the power of mass spectrometry database search. in *Bioinformatics* **40**, i410–i417 (2024). [doi:10.1093/bioinformatics/btae218](https://doi.org/10.1093/bioinformatics/btae218) ## Notes for Citation From 00b4cfef8985885cba26ffe23707f88fa9605191 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 21 Nov 2024 16:36:52 +0000 Subject: [PATCH 07/11] Generate new screengrabs with rich-codex --- docs/images/help.svg | 172 +++++++++++++++++++++---------------------- 1 file changed, 86 insertions(+), 86 deletions(-) diff --git a/docs/images/help.svg b/docs/images/help.svg index 05796ab6..934d3573 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -19,139 +19,139 @@ font-weight: 700; } - .terminal-3568507036-matrix { + .terminal-334567211-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3568507036-title { + .terminal-334567211-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3568507036-r1 { fill: #c5c8c6 } -.terminal-3568507036-r2 { fill: #d0b344 } -.terminal-3568507036-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-3568507036-r4 { fill: #68a0b3;font-weight: bold } -.terminal-3568507036-r5 { fill: #d0b344;font-weight: bold } -.terminal-3568507036-r6 { fill: #608ab1;text-decoration: underline; } -.terminal-3568507036-r7 { fill: #868887 } -.terminal-3568507036-r8 { fill: #98a84b;font-weight: bold } + .terminal-334567211-r1 { fill: #c5c8c6 } +.terminal-334567211-r2 { fill: #d0b344 } +.terminal-334567211-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-334567211-r4 { fill: #68a0b3;font-weight: bold } +.terminal-334567211-r5 { fill: #d0b344;font-weight: bold } +.terminal-334567211-r6 { fill: #608ab1;text-decoration: underline; } +.terminal-334567211-r7 { fill: #868887 } +.terminal-334567211-r8 { fill: #98a84b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -163,46 +163,46 @@ - + - - $ casanovo --help - -Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     - - ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  - ┃                                  Casanovo                                  ┃  - ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  - Casanovo is a state-of-the-art deep learning tool designed for de novo peptide  - sequencing. Powered by a transformer neural network, Casanovo "translates"      - peaks in MS/MS spectra into amino acid sequences.                               - - Links:                                                                          - - • Documentation: https://casanovo.readthedocs.io - • Official code repository: https://github.com/Noble-Lab/casanovo - - If you use Casanovo in your work, please cite:                                  - - • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Melendez, C.F., Nelson, R.,     -Ananth, V., Oh, S. & Noble, W. S. Sequence-to-sequence translation from      -mass spectra to peptides with a transformer model. in Nature Communications  -15, 6427 (2024). doi:10.1038/s41467-024-49731-x                              - - For more information on how to cite different versions of Casanovo, please see  -https://casanovo.readthedocs.io/en/latest/cite.html.                            - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--help-h    Show this message and exit.                                    │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────╮ -│configure Generate a Casanovo configuration file to customize.              │ -│evaluate  Evaluate de novo peptide sequencing performance.                  │ -│sequence  De novo sequence peptides from tandem mass spectra.               │ -│train     Train a Casanovo model on your own data.                          │ -│version   Get the Casanovo version information                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo is a state-of-the-art deep learning tool designed for de novo peptide  + sequencing. Powered by a transformer neural network, Casanovo "translates"      + peaks in MS/MS spectra into amino acid sequences.                               + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io + • Official code repository: https://github.com/Noble-Lab/casanovo + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   +mass spectrometry peptide sequencing with a transformer model. Proceedings   +of the 39th International Conference on Machine Learning - ICML '22 (2022).  +doi:10.1101/2022.02.07.479481.                                               + + For more information on how to cite different versions of Casanovo, please see  +https://casanovo.readthedocs.io/en/latest/cite.html.                            + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│evaluate  Evaluate de novo peptide sequencing performance.                  │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 181fa669832e1d2ac4e9511c280398e73fbd6dbd Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Thu, 21 Nov 2024 17:39:32 +0100 Subject: [PATCH 08/11] Link to paper in CLI --- casanovo/casanovo.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 83d21e2e..71f057f5 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -108,7 +108,8 @@ def main() -> None: - Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo mass spectrometry peptide sequencing with a transformer model. Proceedings of the 39th International Conference on Machine - Learning - ICML '22 (2022). doi:10.1101/2022.02.07.479481. + Learning - ICML '22 (2022). + [link=https://proceedings.mlr.press/v162/yilmaz22a.html]https://proceedings.mlr.press/v162/yilmaz22a.html[/link]. For more information on how to cite different versions of Casanovo, please see [https://casanovo.readthedocs.io/en/latest/cite.html](). From 90edce694ced602fb0abfc2c31a23c26af81e831 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 21 Nov 2024 16:42:28 +0000 Subject: [PATCH 09/11] Generate new screengrabs with rich-codex --- docs/images/help.svg | 182 ++++++++++++++++++++++--------------------- 1 file changed, 93 insertions(+), 89 deletions(-) diff --git a/docs/images/help.svg b/docs/images/help.svg index 934d3573..0597a0df 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + - + - + - - $ casanovo --help - -Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     - - ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  - ┃                                  Casanovo                                  ┃  - ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  - Casanovo is a state-of-the-art deep learning tool designed for de novo peptide  - sequencing. Powered by a transformer neural network, Casanovo "translates"      - peaks in MS/MS spectra into amino acid sequences.                               - - Links:                                                                          - - • Documentation: https://casanovo.readthedocs.io - • Official code repository: https://github.com/Noble-Lab/casanovo - - If you use Casanovo in your work, please cite:                                  - - • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   -mass spectrometry peptide sequencing with a transformer model. Proceedings   -of the 39th International Conference on Machine Learning - ICML '22 (2022).  -doi:10.1101/2022.02.07.479481.                                               - - For more information on how to cite different versions of Casanovo, please see  -https://casanovo.readthedocs.io/en/latest/cite.html.                            - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--help-h    Show this message and exit.                                    │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────╮ -│configure Generate a Casanovo configuration file to customize.              │ -│evaluate  Evaluate de novo peptide sequencing performance.                  │ -│sequence  De novo sequence peptides from tandem mass spectra.               │ -│train     Train a Casanovo model on your own data.                          │ -│version   Get the Casanovo version information                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo is a state-of-the-art deep learning tool designed for de novo peptide  + sequencing. Powered by a transformer neural network, Casanovo "translates"      + peaks in MS/MS spectra into amino acid sequences.                               + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io + • Official code repository: https://github.com/Noble-Lab/casanovo + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   +mass spectrometry peptide sequencing with a transformer model. Proceedings   +of the 39th International Conference on Machine Learning - ICML '22 (2022).  +[link=https://proceedings.mlr.press/v162/yilmaz22a.html]https://proceedings  +.mlr.press/v162/yilmaz22a.html[/link].                                       + + For more information on how to cite different versions of Casanovo, please see  +https://casanovo.readthedocs.io/en/latest/cite.html.                            + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│evaluate  Evaluate de novo peptide sequencing performance.                  │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ + From 821245f68aa76d8288fe5281698c01e06d62c4da Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Thu, 21 Nov 2024 18:16:44 +0100 Subject: [PATCH 10/11] Link didn't work --- casanovo/casanovo.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/casanovo/casanovo.py b/casanovo/casanovo.py index 71f057f5..be3b4d68 100644 --- a/casanovo/casanovo.py +++ b/casanovo/casanovo.py @@ -109,7 +109,7 @@ def main() -> None: De novo mass spectrometry peptide sequencing with a transformer model. Proceedings of the 39th International Conference on Machine Learning - ICML '22 (2022). - [link=https://proceedings.mlr.press/v162/yilmaz22a.html]https://proceedings.mlr.press/v162/yilmaz22a.html[/link]. + [https://proceedings.mlr.press/v162/yilmaz22a.html](). For more information on how to cite different versions of Casanovo, please see [https://casanovo.readthedocs.io/en/latest/cite.html](). From 0b7505afe0844013ca657de81040d4fb2f3015c0 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 21 Nov 2024 17:19:58 +0000 Subject: [PATCH 11/11] Generate new screengrabs with rich-codex --- docs/images/help.svg | 182 +++++++++++++++++++++---------------------- 1 file changed, 89 insertions(+), 93 deletions(-) diff --git a/docs/images/help.svg b/docs/images/help.svg index 0597a0df..6cf269bb 100644 --- a/docs/images/help.svg +++ b/docs/images/help.svg @@ -1,4 +1,4 @@ - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - + - + - - $ casanovo --help - -Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     - - ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  - ┃                                  Casanovo                                  ┃  - ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  - Casanovo is a state-of-the-art deep learning tool designed for de novo peptide  - sequencing. Powered by a transformer neural network, Casanovo "translates"      - peaks in MS/MS spectra into amino acid sequences.                               - - Links:                                                                          - - • Documentation: https://casanovo.readthedocs.io - • Official code repository: https://github.com/Noble-Lab/casanovo - - If you use Casanovo in your work, please cite:                                  - - • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   -mass spectrometry peptide sequencing with a transformer model. Proceedings   -of the 39th International Conference on Machine Learning - ICML '22 (2022).  -[link=https://proceedings.mlr.press/v162/yilmaz22a.html]https://proceedings  -.mlr.press/v162/yilmaz22a.html[/link].                                       - - For more information on how to cite different versions of Casanovo, please see  -https://casanovo.readthedocs.io/en/latest/cite.html.                            - -╭─ Options ────────────────────────────────────────────────────────────────────╮ -│--help-h    Show this message and exit.                                    │ -╰──────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────╮ -│configure Generate a Casanovo configuration file to customize.              │ -│evaluate  Evaluate de novo peptide sequencing performance.                  │ -│sequence  De novo sequence peptides from tandem mass spectra.               │ -│train     Train a Casanovo model on your own data.                          │ -│version   Get the Casanovo version information                              │ -╰──────────────────────────────────────────────────────────────────────────────╯ - + + $ casanovo --help + +Usage:casanovo [OPTIONS] COMMAND [ARGS]...                                     + + ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓  + ┃                                  Casanovo                                  ┃  + ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛  + Casanovo is a state-of-the-art deep learning tool designed for de novo peptide  + sequencing. Powered by a transformer neural network, Casanovo "translates"      + peaks in MS/MS spectra into amino acid sequences.                               + + Links:                                                                          + + • Documentation: https://casanovo.readthedocs.io + • Official code repository: https://github.com/Noble-Lab/casanovo + + If you use Casanovo in your work, please cite:                                  + + • Yilmaz, M., Fondrie, W. E., Bittremieux, W., Oh, S. & Noble, W. S. De novo   +mass spectrometry peptide sequencing with a transformer model. Proceedings   +of the 39th International Conference on Machine Learning - ICML '22 (2022).  +https://proceedings.mlr.press/v162/yilmaz22a.html.                           + + For more information on how to cite different versions of Casanovo, please see  +https://casanovo.readthedocs.io/en/latest/cite.html.                            + +╭─ Options ────────────────────────────────────────────────────────────────────╮ +│--help-h    Show this message and exit.                                    │ +╰──────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────╮ +│configure Generate a Casanovo configuration file to customize.              │ +│evaluate  Evaluate de novo peptide sequencing performance.                  │ +│sequence  De novo sequence peptides from tandem mass spectra.               │ +│train     Train a Casanovo model on your own data.                          │ +│version   Get the Casanovo version information                              │ +╰──────────────────────────────────────────────────────────────────────────────╯ +