Prediction models

Pre-trained MS²PIP models

MS²PIP includes multiple specialized prediction models, fit for peptide spectra with different properties. These properties include fragmentation method, instrument, labeling techniques and modifications. As all of these properties can influence fragmentation patterns, it is important to match the MS²PIP model to the properties of your experimental dataset.

All models are downloaded automatically upon first use. Model files can also be downloaded manually from genesis.ugent.be/uvpublicdata/ms2pip.

MS2 acquisition information and peptide properties of the models’ training datasets:

Model	Fragmentation method	MS2 mass analyzer	Peptide properties
HCD2019	HCD	Orbitrap	Tryptic digest
HCD2021	HCD	Orbitrap	Tryptic / Chymotrypsin digest
CID	CID	Linear ion trap	Tryptic digest
iTRAQ	HCD	Orbitrap	Tryptic digest, iTRAQ-labeled
iTRAQphospho	HCD	Orbitrap	Tryptic digest, iTRAQ-labeled, enriched for phosphorylation
TMT	HCD	Orbitrap	Tryptic digest, TMT-labeled
TTOF5600	CID	Quadrupole time-of-flight	Tryptic digest
HCDch2	HCD	Orbitrap	Tryptic digest
CIDch2	CID	Linear ion trap	Tryptic digest
Immuno-HCD	HCD	Orbitrap	Immunopeptides
CID-TMT	CID	Linear ion trap	Tryptic digest, TMT-labeled
timsTOF2023	CID	Ion mobility quadrupole time-of-flight	Tryptic-, elastase digest, immuno class 1
timsTOF2024	CID	Ion mobility quadrupole time-of-flight	Tryptic-, elastase digest, immuno class 1 & class 2

Models, version numbers, and the train and test datasets used to create each model:

Model	Current version	Train-test dataset (unique peptides)	Evaluation dataset (unique peptides)	Median Pearson correlation on evaluation dataset
HCD2019	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 (+) 0.644162 (++)
CIDch2	v20190107	NIST CID Human (340 356)	NIST CID Yeast (92 609)	0.904947 (+) 0.813342 (++)
HCD2021	v20210416	Combined dataset (520 579)	PXD008034 (35 269)	0.932361
Immuno-HCD	v20210316	Combined dataset (460 191)	PXD005231 (HLA-I) (46 753) PXD020011 (HLA-II) (23 941)	0.963736
CID-TMT	v20220104	PXD041002 (72 138)	PXD005890 (69 768)	0.851085
timsTOF2023	v20230912	Combined dataset (234 973)	PXD043026 PXD046535 PXD046543	0.892540 (tryptic) 0.871258 (elastase) 0.899834 (class I) 0.635548 (class II)
timsTOF2024	v20240105	Combined dataset (480 024)	PXD043026 PXD046535 PXD046543 PXD038782	0.883270 (tryptic) 0.814374 (elastase) 0.887192 (class I) 0.847951 (class II)

Training new MS²PIP models

[todo]

Prediction features

The table below lists and describes all features generated and used by MS²PIP. These are mostly based on four amino acid properties (basicity, hydrophobicity, helicity and isoelectric point) for the full precursor and for the N- and C-terminal ions.

Feature	Description
p_length	Precursor length
p_charge	Precursor charge
p_charge1	Precursor charge is 1 (one-hot encoding)
p_charge2	Precursor charge is 2 (one-hot encoding)
p_charge3	Precursor charge is 3 (one-hot encoding)
p_charge4	Precursor charge is 4 (one-hot encoding)
p_charge5	Precursor charge is 5 (one-hot encoding)
p_basi_min	Minimum basicity of the precursor
p_basi_q1	First quartile of basicity of the precursor
p_basi_q2	Second quartile of basicity of the precursor
p_basi_q3	Third quartile of basicity of the precursor
p_basi_max	Maximum basicity of the precursor
p_heli_min	Minimum helicity of the precursor
p_heli_q1	First quartile of helicity of the precursor
p_heli_q2	Second quartile of helicity of the precursor
p_heli_q3	Third quartile of helicity of the precursor
p_heli_max	Maximum helicity of the precursor
p_hydro_min	Minimum hydrophobicity of the precursor
p_hydro_q1	First quartile of hydrophobicity of the precursor
p_hydro_q2	Second quartile of hydrophobicity of the precursor
p_hydro_q3	Third quartile of hydrophobicity of the precursor
p_hydro_max	Maximum hydrophobicity of the precursor
p_iso_min	Minimum isoelectric point of the precursor
p_iso_q1	First quartile of isoelectric point of the precursor
p_iso_q2	Second quartile of isoelectric point of the precursor
p_iso_q3	Third quartile of isoelectric point of the precursor
p_iso_max	Maximum isoelectric point of the precursor
n_length	Length of the N-terminal ion
c_length	Length of the C-terminal ion
n_count_A	Count of amino acid ‘A’ in the N-terminal ion
c_count_A	Count of amino acid ‘A’ in the C-terminal ion
n_count_C	Count of amino acid ‘C’ in the N-terminal ion
c_count_C	Count of amino acid ‘C’ in the C-terminal ion
n_count_D	Count of amino acid ‘D’ in the N-terminal ion
c_count_D	Count of amino acid ‘D’ in the C-terminal ion
n_count_E	Count of amino acid ‘E’ in the N-terminal ion
c_count_E	Count of amino acid ‘E’ in the C-terminal ion
n_count_F	Count of amino acid ‘F’ in the N-terminal ion
c_count_F	Count of amino acid ‘F’ in the C-terminal ion
n_count_G	Count of amino acid ‘G’ in the N-terminal ion
c_count_G	Count of amino acid ‘G’ in the C-terminal ion
n_count_H	Count of amino acid ‘H’ in the N-terminal ion
c_count_H	Count of amino acid ‘H’ in the C-terminal ion
n_count_I	Count of amino acid ‘I’ in the N-terminal ion
c_count_I	Count of amino acid ‘I’ in the C-terminal ion
n_count_K	Count of amino acid ‘K’ in the N-terminal ion
c_count_K	Count of amino acid ‘K’ in the C-terminal ion
n_count_M	Count of amino acid ‘M’ in the N-terminal ion
c_count_M	Count of amino acid ‘M’ in the C-terminal ion
n_count_N	Count of amino acid ‘N’ in the N-terminal ion
c_count_N	Count of amino acid ‘N’ in the C-terminal ion
n_count_P	Count of amino acid ‘P’ in the N-terminal ion
c_count_P	Count of amino acid ‘P’ in the C-terminal ion
n_count_Q	Count of amino acid ‘Q’ in the N-terminal ion
c_count_Q	Count of amino acid ‘Q’ in the C-terminal ion
n_count_R	Count of amino acid ‘R’ in the N-terminal ion
c_count_R	Count of amino acid ‘R’ in the C-terminal ion
n_count_S	Count of amino acid ‘S’ in the N-terminal ion
c_count_S	Count of amino acid ‘S’ in the C-terminal ion
n_count_T	Count of amino acid ‘T’ in the N-terminal ion
c_count_T	Count of amino acid ‘T’ in the C-terminal ion
n_count_V	Count of amino acid ‘V’ in the N-terminal ion
c_count_V	Count of amino acid ‘V’ in the C-terminal ion
n_count_W	Count of amino acid ‘W’ in the N-terminal ion
c_count_W	Count of amino acid ‘W’ in the C-terminal ion
n_count_Y	Count of amino acid ‘Y’ in the N-terminal ion
c_count_Y	Count of amino acid ‘Y’ in the C-terminal ion
p0_basi	basicity of the first amino acid of the peptide
p-1_basi	basicity of the last amino acid of the peptide
pi-1_basi	basicity of the amino acid before the fragmentation site
pi_basi	basicity of the amino acid at the fragmentation site
pi+1_basi	basicity of the 1st amino acid after the fragmentation site
pi+2_basi	basicity of the 2nd amino acid after the fragmentation site
n_basi_sum	Sum of basicity of the N-terminal ion
n_basi_min	Minimum basicity of the N-terminal ion
n_basi_q1	First quartile of basicity of the N-terminal ion
n_basi_q2	Second quartile of basicity of the N-terminal ion
n_basi_q3	Third quartile of basicity of the N-terminal ion
n_basi_max	Maximum basicity of the N-terminal ion
c_basi_sum	Sum of basicity of the C-terminal ion
c_basi_min	Minimum basicity of the C-terminal ion
c_basi_q1	First quartile of basicity of the C-terminal ion
c_basi_q2	Second quartile of basicity of the C-terminal ion
c_basi_q3	Third quartile of basicity of the C-terminal ion
c_basi_max	Maximum basicity of the C-terminal ion
p0_heli	Helicity of the first amino acid of the peptide
p-1_heli	Helicity of the last amino acid of the peptide
pi-1_heli	Helicity of the amino acid before the fragmentation site
pi_heli	Helicity of the amino acid at the fragmentation site
pi+1_heli	Helicity of the 1st amino acid after the fragmentation site
pi+2_heli	Helicity of the 2nd amino acid after the fragmentation site
n_heli_sum	Sum of helicity of the N-terminal ion
n_heli_min	Minimum helicity of the N-terminal ion
n_heli_q1	First quartile of helicity of the N-terminal ion
n_heli_q2	Second quartile of helicity of the N-terminal ion
n_heli_q3	Third quartile of helicity of the N-terminal ion
n_heli_max	Maximum helicity of the N-terminal ion
c_heli_sum	Sum of helicity of the C-terminal ion
c_heli_min	Minimum helicity of the C-terminal ion
c_heli_q1	First quartile of helicity of the C-terminal ion
c_heli_q2	Second quartile of helicity of the C-terminal ion
c_heli_q3	Third quartile of helicity of the C-terminal ion
c_heli_max	Maximum helicity of the C-terminal ion
p0_hydro	Hydrophobicity of the first amino acid of the peptide
p-1_hydro	Hydrophobicity of the last amino acid of the peptide
pi-1_hydro	Hydrophobicity of the amino acid before the fragmentation site
pi_hydro	Hydrophobicity of the amino acid at the fragmentation site
pi+1_hydro	Hydrophobicity of the 1st amino acid after the fragmentation site
pi+2_hydro	Hydrophobicity of the 2nd amino acid after the fragmentation site
n_hydro_sum	Sum of hydrophobicity of the N-terminal ion
n_hydro_min	Minimum hydrophobicity of the N-terminal ion
n_hydro_q1	First quartile of hydrophobicity of the N-terminal ion
n_hydro_q2	Second quartile of hydrophobicity of the N-terminal ion
n_hydro_q3	Third quartile of hydrophobicity of the N-terminal ion
n_hydro_max	Maximum hydrophobicity of the N-terminal ion
c_hydro_sum	Sum of hydrophobicity of the C-terminal ion
c_hydro_min	Minimum hydrophobicity of the C-terminal ion
c_hydro_q1	First quartile of hydrophobicity of the C-terminal ion
c_hydro_q2	Second quartile of hydrophobicity of the C-terminal ion
c_hydro_q3	Third quartile of hydrophobicity of the C-terminal ion
c_hydro_max	Maximum hydrophobicity of the C-terminal ion
p0_iso	Isoelectric point of the first amino acid of the peptide
p-1_iso	Isoelectric point of the last amino acid of the peptide
pi-1_iso	Isoelectric point of the amino acid before the fragmentation site
pi_iso	Isoelectric point of the amino acid at the fragmentation site
pi+1_iso	Isoelectric point of the 1st amino acid after the fragmentation site
pi+2_iso	Isoelectric point of the 2nd amino acid after the fragmentation site
n_iso_sum	Sum of isoelectric points of the N-terminal ion
n_iso_min	Minimum isoelectric point of the N-terminal ion
n_iso_q1	First quartile of isoelectric points of the N-terminal ion
n_iso_q2	Second quartile of isoelectric points of the N-terminal ion
n_iso_q3	Third quartile of isoelectric points of the N-terminal ion
n_iso_max	Maximum isoelectric point of the N-terminal ion
c_iso_sum	Sum of isoelectric points of the C-terminal ion
c_iso_min	Minimum isoelectric point of the C-terminal ion
c_iso_q1	First quartile of isoelectric points of the C-terminal ion
c_iso_q2	Second quartile of isoelectric points of the C-terminal ion
c_iso_q3	Third quartile of isoelectric points of the C-terminal ion
c_iso_max	Maximum isoelectric point of the C-terminal ion