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v3.6.0

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@RalfG RalfG released this 30 Mar 16:33
v3.6.0
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Learn about vigilant mode.

New since previous release:

  • DeepLC integration! Predict spectral libraries with accurate LC retention time prediction, even for modified peptides. Enable DeepLC with the -r flag in MS²PIP or by adding "add_retention_time":true to the fasta2speclib configuration.
  • Additional support for TOML-based configuration files: see config.toml example
  • New Skyline .blib to PEPREC and MGF converter script in conversion_tools
  • Various under-the-hood improvements

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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