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Releases: compomics/ms2pip

v3.5.0

04 Mar 13:16
@RalfG RalfG
v3.5.0
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v3.5.0

New since last release:

  • ProteinId column added to Spectronaut CSV output
  • Major code refactoring
  • Improved logging
  • Improved exception handling
  • Faster 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 (1 623 712) PXD008034 (35 269) 0.903786
CID v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947
iTRAQ v20190107 NIST iTRAQ (704 041) PXD001189 (41 502) 0.905870
iTRAQphospho v20190107 NIST iTRAQ phospho (183 383) PXD001189 (9 088) 0.843898
TMT v20190107 Peng Lab TMT Spectral Library (1 185 547) PXD009495 (36 137) 0.950460
TTOF5600 v20190107 PXD000954 (215 713) PXD001587 (15 111) 0.746823
HCDch2 v20190107 MassIVE-KB (1 623 712) PXD008034 (35 269) 0.903786 (+) and 0.644162 (++)
CIDch2 v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947 (+) and 0.813342 (++)
Assets 2
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v3.4.2

31 Dec 15:07
@RalfG RalfG
v3.4.2
cb388c4
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v3.4.2

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 (1 623 712) PXD008034 (35 269) 0.903786
CID v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947
iTRAQ v20190107 NIST iTRAQ (704 041) PXD001189 (41 502) 0.905870
iTRAQphospho v20190107 NIST iTRAQ phospho (183 383) PXD001189 (9 088) 0.843898
TMT v20190107 Peng Lab TMT Spectral Library (1 185 547) PXD009495 (36 137) 0.950460
TTOF5600 v20190107 PXD000954 (215 713) PXD001587 (15 111) 0.746823
HCDch2 v20190107 MassIVE-KB (1 623 712) PXD008034 (35 269) 0.903786 (+) and 0.644162 (++)
CIDch2 v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947 (+) and 0.813342 (++)
Assets 2
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v20191029

29 Oct 17:39
@RalfG RalfG
v20191029
0ccc204
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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 (1 623 712) PXD008034 (35 269) 0.903786
CID v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947
iTRAQ v20190107 NIST iTRAQ (704 041) PXD001189 (41 502) 0.905870
iTRAQphospho v20190107 NIST iTRAQ phospho (183 383) PXD001189 (9 088) 0.843898
TMT v20190107 Peng Lab TMT Spectral Library (1 185 547) PXD009495 (36 137) 0.950460
TTOF5600 v20190107 PXD000954 (215 713) PXD001587 (15 111) 0.746823
HCDch2 v20190107 MassIVE-KB (1 623 712) PXD008034 (35 269) 0.903786 (+) and 0.644162 (++)
CIDch2 v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947 (+) and 0.813342 (++)
Assets 2
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v20190624

23 Jun 15:46
@RalfG RalfG
v20190624
4f744c5
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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 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 (1 623 712) PXD008034 (35 269) 0.903786
CID v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947
iTRAQ v20190107 NIST iTRAQ (704 041) PXD001189 (41 502) 0.905870
iTRAQphospho v20190107 NIST iTRAQ phospho (183 383) PXD001189 (9 088) 0.843898
TMT v20190107 Peng Lab TMT Spectral Library (1 185 547) PXD009495 (36 137) 0.950460
TTOF5600 v20190107 PXD000954 (215 713) PXD001587 (15 111) 0.746823
HCDch2 v20190107 MassIVE-KB (1 623 712) PXD008034 (35 269) 0.903786 (+) and 0.644162 (++)
CIDch2 v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947 (+) and 0.813342 (++)
Assets 3
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v20190312

12 Mar 19:32
@RalfG RalfG
v20190312
bc221cd
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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 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 (1 623 712) PXD008034 (35 269) 0.903786
CID v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947
iTRAQ v20190107 NIST iTRAQ (704 041) PXD001189 (41 502) 0.905870
iTRAQphospho v20190107 NIST iTRAQ phospho (183 383) PXD001189 (9 088) 0.843898
TMT v20190107 Peng Lab TMT Spectral Library (1 185 547) PXD009495 (36 137) 0.950460
TTOF5600 v20190107 PXD000954 (215 713) PXD001587 (15 111) 0.746823
HCDch2 v20190107 MassIVE-KB (1 623 712) PXD008034 (35 269) 0.903786 (+) and 0.644162 (++)
CIDch2 v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947 (+) and 0.813342 (++)
Assets 3
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v20190130

30 Jan 19:50
@RalfG RalfG
v20190130
74be8e1
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v20190130

New since last release:

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 (1 623 712) PXD008034 (35 269) 0.903786
CID v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947
iTRAQ v20190107 NIST iTRAQ (704 041) PXD001189 (41 502) 0.905870
iTRAQphospho v20190107 NIST iTRAQ phospho (183 383) PXD001189 (9 088) 0.843898
TMT v20190107 Peng Lab TMT Spectral Library (1 185 547) PXD009495 (36 137) 0.950460
TTOF5600 v20190107 PXD000954 (215 713) PXD001587 (15 111) 0.746823
Assets 3
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v20190120

20 Jan 17:45
@RalfG RalfG
v20190120
e4c9e3b
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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 (1 623 712) PXD008034 (35 269) 0.903786
CID v20190107 NIST CID Human (340 356) NIST CID Yeast (92 609) 0.904947
iTRAQ v20190107 NIST iTRAQ (704 041) PXD001189 (41 502) 0.905870
iTRAQphospho v20190107 NIST iTRAQ phospho (183 383) PXD001189 (9 088) 0.843898
TMT v20190107 Peng Lab TMT Spectral Library (1 185 547) PXD009495 (36 137) 0.950460
TTOF5600 v20190107 PXD000954 (215 713) PXD001587 (15 111) 0.746823
Assets 2
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