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 (++)

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 (++)

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 (++)

v20190130

New since last release:

• Bugfixes
• Updated requirements.txt
• Includes precompiled files 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

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