Update models docs

compomics · Dec 11, 2023 · a8c61b4 · a8c61b4
1 parent aca9fd3
commit a8c61b4
Showing 1 changed file with 30 additions and 27 deletions.
diff --git a/docs/source/prediction-models.rst b/docs/source/prediction-models.rst
@@ -15,32 +15,34 @@ from `genesis.ugent.be/uvpublicdata/ms2pip <https://genesis.ugent.be/uvpublicdat
 
 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                        |
-+--------------+----------------------+---------------------------+----------------------------------------------------+
++--------------+----------------------+----------------------------------------+----------------------------------------------------+
+| 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                        |
++--------------+----------------------+----------------------------------------+----------------------------------------------------+
+| timsTOF      | CID                  | Ion mobility quadrupole time-of-flight | Tryptic digest, TMT-labeled                        |
++--------------+----------------------+----------------------------------------+----------------------------------------------------+
 
 Models, version numbers, and the train and test datasets used to create each model:
 
@@ -69,7 +71,7 @@ Models, version numbers, and the train and test datasets used to create each mod
 | Immuno-HCD    | v20210316         | Combined dataset (460 191)                      | `PXD005231 (HLA-I)`_ (46 753)                     | 0.963736                                |
 |               |                   |                                                 | `PXD020011 (HLA-II)`_ (23 941)                    |                                         |
 +---------------+-------------------+-------------------------------------------------+---------------------------------------------------+-----------------------------------------+
-| CID-TMT       | v20220104         | in-house dataset (72 138)                       | `PXD005890`_ (69 768)                             | 0.851085                                |
+| CID-TMT       | v20220104         | `PXD041002`_ (72 138)                           | `PXD005890`_ (69 768)                             | 0.851085                                |
 +---------------+-------------------+-------------------------------------------------+---------------------------------------------------+-----------------------------------------+
 
 
@@ -92,5 +94,6 @@ Training new MS²PIP models
 .. _PXD001587: https://doi.org/10.1038/nmeth.3255
 .. _PXD005231 (HLA-I): https://doi.org/10.1101/098780
 .. _PXD020011 (HLA-II): https://doi.org/10.3389/fimmu.2020.01981
+.. _PXD041002: https://doi.org/10.1093/nar/gkad335
 .. _PXD005890: https://doi.org/10.1021/acs.jproteome.7b00091
 .. _Training new MS²PIP models: http://compomics.github.io/projects/ms2pip_c/wiki/Training-new-MS2PIP-models.html