New since last release:
- MS²PIP can now be downloaded and installed from PyPI using `pip install ms2pip`. MS²PIP on PyPI is already compiled, so it can be installed in seconds (without slow and memory inefficient compilation step).
- MS²PIP will use all available CPUs by default.
- Speed improvements after multiprocessing step (especially for large numbers of predictions).
- Moved to semantic versioning
Includes the following models:
Model | Current version | Train-test dataset (unique peptides) | Evaluation dataset (unique peptides) | Median Pearson correlation on evaluation dataset
-|-|-|-|-
HCD | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786
CID | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947
iTRAQ | v20190107 | [NIST iTRAQ](https://chemdata.nist.gov/) (704 041) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (41 502) | 0.905870
iTRAQphospho | v20190107 | [NIST iTRAQ phospho](https://chemdata.nist.gov/) (183 383) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (9 088) | 0.843898
TMT | v20190107 | [Peng Lab TMT Spectral Library](https://doi.org/10.1021/acs.jproteome.8b00594) (1 185 547) | [PXD009495](https://doi.org/10.15252/msb.20188242) (36 137) | 0.950460
TTOF5600 | v20190107 | [PXD000954](https://doi.org/10.1038/sdata.2014.31) (215 713) | [PXD001587](https://doi.org/10.1038/nmeth.3255) (15 111) | 0.746823
HCDch2 | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786 (+) and 0.644162 (++)
CIDch2 | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947 (+) and 0.813342 (++)
v20191029
New since last release:
- MS²PIP is now locally installable with pip and conda
- New: Spectronaut CSV and Bibliospec/Skyline output formats
- Output formats can now be specified in the config file (e.g. out=csv,msp,spectronaut)
- Slightly faster model compilation
Includes the following models:
Model | Current version | Train-test dataset (unique peptides) | Evaluation dataset (unique peptides) | Median Pearson correlation on evaluation dataset
-|-|-|-|-
HCD | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786
CID | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947
iTRAQ | v20190107 | [NIST iTRAQ](https://chemdata.nist.gov/) (704 041) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (41 502) | 0.905870
iTRAQphospho | v20190107 | [NIST iTRAQ phospho](https://chemdata.nist.gov/) (183 383) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (9 088) | 0.843898
TMT | v20190107 | [Peng Lab TMT Spectral Library](https://doi.org/10.1021/acs.jproteome.8b00594) (1 185 547) | [PXD009495](https://doi.org/10.15252/msb.20188242) (36 137) | 0.950460
TTOF5600 | v20190107 | [PXD000954](https://doi.org/10.1038/sdata.2014.31) (215 713) | [PXD001587](https://doi.org/10.1038/nmeth.3255) (15 111) | 0.746823
HCDch2 | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786 (+) and 0.644162 (++)
CIDch2 | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947 (+) and 0.813342 (++)
v20190624
New since previous release:
- Add 'RetentionTimeMins' to MSP output, if ELUDE model file is given.
Includes precompiled files: `ms2pip_c_v20190624_precompiled_cython_modules.zip` (See the [Extended Install Instructions](https://github.com/compomics/ms2pip_c/wiki/Extended_install_instructions) for more information)
Includes the following models:
Model | Current version | Train-test dataset (unique peptides) | Evaluation dataset (unique peptides) | Median Pearson correlation on evaluation dataset
-|-|-|-|-
HCD | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786
CID | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947
iTRAQ | v20190107 | [NIST iTRAQ](https://chemdata.nist.gov/) (704 041) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (41 502) | 0.905870
iTRAQphospho | v20190107 | [NIST iTRAQ phospho](https://chemdata.nist.gov/) (183 383) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (9 088) | 0.843898
TMT | v20190107 | [Peng Lab TMT Spectral Library](https://doi.org/10.1021/acs.jproteome.8b00594) (1 185 547) | [PXD009495](https://doi.org/10.15252/msb.20188242) (36 137) | 0.950460
TTOF5600 | v20190107 | [PXD000954](https://doi.org/10.1038/sdata.2014.31) (215 713) | [PXD001587](https://doi.org/10.1038/nmeth.3255) (15 111) | 0.746823
HCDch2 | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786 (+) and 0.644162 (++)
CIDch2 | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947 (+) and 0.813342 (++)
v20190312
New since last release:
- Included models for charge 2 fragment ions (CID and HCD)
Includes precompiled files : `ms2pip_c_v20190312_precompiled_cython_modules.zip` (See the [Extended Install Instructions](https://github.com/compomics/ms2pip_c/wiki/Extended_install_instructions) for more information)
Includes the following models:
Model | Current version | Train-test dataset (unique peptides) | Evaluation dataset (unique peptides) | Median Pearson correlation on evaluation dataset
-|-|-|-|-
HCD | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786
CID | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947
iTRAQ | v20190107 | [NIST iTRAQ](https://chemdata.nist.gov/) (704 041) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (41 502) | 0.905870
iTRAQphospho | v20190107 | [NIST iTRAQ phospho](https://chemdata.nist.gov/) (183 383) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (9 088) | 0.843898
TMT | v20190107 | [Peng Lab TMT Spectral Library](https://doi.org/10.1021/acs.jproteome.8b00594) (1 185 547) | [PXD009495](https://doi.org/10.15252/msb.20188242) (36 137) | 0.950460
TTOF5600 | v20190107 | [PXD000954](https://doi.org/10.1038/sdata.2014.31) (215 713) | [PXD001587](https://doi.org/10.1038/nmeth.3255) (15 111) | 0.746823
HCDch2 | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786 (+) and 0.644162 (++)
CIDch2 | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947 (+) and 0.813342 (++)
v20190130
New since last release:
- Bugfixes
- Updated requirements.txt
- Includes precompiled files see the [Extended Install Instructions](https://github.com/compomics/ms2pip_c/wiki/Extended_install_instructions) for more information
Includes the following models:
Model | Current version | Train-test dataset (unique peptides) | Evaluation dataset (unique peptides) | Median Pearson correlation on evaluation dataset
-|-|-|-|-
HCD | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786
CID | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947
iTRAQ | v20190107 | [NIST iTRAQ](https://chemdata.nist.gov/) (704 041) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (41 502) | 0.905870
iTRAQphospho | v20190107 | [NIST iTRAQ phospho](https://chemdata.nist.gov/) (183 383) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (9 088) | 0.843898
TMT | v20190107 | [Peng Lab TMT Spectral Library](https://doi.org/10.1021/acs.jproteome.8b00594) (1 185 547) | [PXD009495](https://doi.org/10.15252/msb.20188242) (36 137) | 0.950460
TTOF5600 | v20190107 | [PXD000954](https://doi.org/10.1038/sdata.2014.31) (215 713) | [PXD001587](https://doi.org/10.1038/nmeth.3255) (15 111) | 0.746823
v20190120
First official GitHub release of the third iteration of MS2PIP, called MS2PIPc.
Includes the following models:
Model | Current version | Train-test dataset (unique peptides) | Evaluation dataset (unique peptides) | Median Pearson correlation on evaluation dataset
-|-|-|-|-
HCD | v20190107 | [MassIVE-KB](https://doi.org/10.1016/j.cels.2018.08.004) (1 623 712) | [PXD008034](https://doi.org/10.1016/j.jprot.2017.12.006) (35 269) | 0.903786
CID | v20190107 | [NIST CID Human](https://chemdata.nist.gov/) (340 356) | [NIST CID Yeast](https://chemdata.nist.gov/) (92 609) | 0.904947
iTRAQ | v20190107 | [NIST iTRAQ](https://chemdata.nist.gov/) (704 041) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (41 502) | 0.905870
iTRAQphospho | v20190107 | [NIST iTRAQ phospho](https://chemdata.nist.gov/) (183 383) | [PXD001189](https://doi.org/10.1182/blood-2016-05-714048) (9 088) | 0.843898
TMT | v20190107 | [Peng Lab TMT Spectral Library](https://doi.org/10.1021/acs.jproteome.8b00594) (1 185 547) | [PXD009495](https://doi.org/10.15252/msb.20188242) (36 137) | 0.950460
TTOF5600 | v20190107 | [PXD000954](https://doi.org/10.1038/sdata.2014.31) (215 713) | [PXD001587](https://doi.org/10.1038/nmeth.3255) (15 111) | 0.746823