Merge pull request #16 from hgb-bin-proteomics/develop

Release MS Annika 2.0 v2.2.1

Author: michabirklbauer

HISTORY.md

@@ -1,5 +1,20 @@
 # History
 
+## MS Annika 2.0 v2.2.1
+
+- Release date: 18. September 2023
+- Supported Proteome Discoverer versions: 3.1
+- Changes:
+  - Minor:
+    - Added a retention time window parameter for MS3 search
+    - Added the number of found doublets to the CSM result table
+    - Changed the default values of several parameters to better reflect current cross-linking workflows
+    - Added a charge determination algorithm for calculating missing fragment ion charge states
+  - Bugfixes:
+    - Fixed a bug in relation to N-terminal protein modifications in the internal MS Amanda version
+    - Fixed a bug that prevented reading of MGF and timsTOF files
+    - Fixed a bug that prevented associating MSn scans with peptide hits and therefore led to improper usage of the MS3 rescoring function and spectrum display in Proteome Discoverer
+
 ## MS Annika 2.0 v1.2.0
 
 - Release date: 12. May 2023

MS_Annika_2.0_UserManual.pdf

@@ -18,22 +18,48 @@ A list of changes in every version can be found in [HISTORY.md](https://github.c
 
 A tutorial of how to use MS Annika 2.0 can be found here: [Text](https://github.com/hgb-bin-proteomics/MSAnnika/blob/master/tutorial/MS_Annika_2.0_Tutorial.pdf) / [Video](https://www.youtube.com/watch?v=L1lVt35PYv4)
 
+## Example Files
+
+Example files to try MS Annika 2.0 can either be downloaded from [PRIDE](https://www.ebi.ac.uk/pride/archive/projects/PXD041955) or directly here:
+- Minimal example for MS2 search: [MGF + fasta](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/examples/data.zip)
+- RAW file for MS3 search: [RAW](https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/08/PXD041955/20211219_Eclipse_LC4_G2_Trap_backflash_Peplib20_DSSO_pl1_MS3_OTOTOT.raw)
+
 ## Example Workflows
 
-Example workflows that can be used in Proteome Discoverer*:
+Example workflows that can be used in Proteome Discoverer:
 
 - Proteome Discoverer 3.0 / 3.1:
   - DSSO MS2 search (CID, ETD, HCD, stepped HCD): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2.zip)
   - DSSO MS2-MS3 search (MS3 recorded in the orbitrap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Orbitrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Orbitrap.zip)
   - DSSO MS2-MS3 search (MS3 recorded in the ion trap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Iontrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_MS2_MS3_Iontrap.zip)
+  - DSBSO MS2 search (CID, ETD, HCD, stepped HCD): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSBSO_MS2.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSBSO_MS2.zip)
+  - DSBSO MS2-MS3 search (MS3 recorded in the orbitrap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSBSO_MS2_MS3_Orbitrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSBSO_MS2_MS3_Orbitrap.zip)
+  - DSBSO MS2-MS3 search (MS3 recorded in the ion trap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSBSO_MS2_MS3_Iontrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSBSO_MS2_MS3_Iontrap.zip)
 - Proteome Discoverer 2.5:
   - DSSO MS2 search (CID, ETD, HCD, stepped HCD): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD2.5/DSSO_MS2.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD2.5/DSSO_MS2.zip)
   - DSSO MS2-MS3 search (MS3 recorded in the orbitrap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD2.5/DSSO_MS2_MS3_Orbitrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD2.5/DSSO_MS2_MS3_Orbitrap.zip)
   - DSSO MS2-MS3 search (MS3 recorded in the ion trap): [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD2.5/DSSO_MS2_MS3_Iontrap.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD2.5/DSSO_MS2_MS3_Iontrap.zip)
 
+The provided workflows also require the installation of [MS Amanda](https://dx.doi.org/10.1021/pr500202e) which can be downloaded [here](https://ms.imp.ac.at/?action=ms-amanda).
+
 The general processing workflow for almost any crosslink search is depicted [here](workflows/general_wf.png).
 
-*The provided workflows also require the installation of [MS Amanda](https://dx.doi.org/10.1021/pr500202e) which can be downloaded [here](https://ms.imp.ac.at/?action=ms-amanda).
+For MS2 searches (CID, ETD, HCD, stepped HCD) it can also be beneficial to employ the [IMP MS2 Spectrum Processor](https://ms.imp.ac.at/?action=spectrum-processor) node, an example workflow for Proteome Discoverer 3.0 is given here:
+
+- DSSO MS2 search with IMP MS2 Spectrum Processor: [pdAnalysis](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_IMP_MS2.pdAnalysis) / [zip](https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/workflows/PD3.0/DSSO_IMP_MS2.zip)
+
+This workflow additionally requires the installation of the [IMP MS2 Spectrum Processor](https://ms.imp.ac.at/?action=spectrum-processor) node beforehand, which can be directly downloaded from [here](https://ms.imp.ac.at/?file=spectrum-processor/ms2spectrumprocessor_3.0.zip).
+
+## Support for MGF and timsTOF Data
+
+The following MS Annika versions support MGF\* and timsTOF\*\* data input:
+- Proteome Discoverer 3.1: [MS Annika 2.0 v2.2.1](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v2.2.1)
+- Proteome Discoverer 3.0: [MS Annika 2.0 v1.1.4fix](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v1.1.4fix)
+- Proteome Discoverer <=2.5: [MS Annika 1.0 v1.0.0](https://github.com/hgb-bin-proteomics/MSAnnika/releases/tag/v1.0.0)\*\*\*
+
+\*MS Annika 2.0 only supports MS2 search for MGF files since MGF files don't contain sufficient MS3 information.  
+\*\*requires installation of the Bruker Ion Mobility reader.  
+\*\*\*requires installation of the [IMP MS2 Spectrum Processor](https://ms.imp.ac.at/?action=spectrum-processor) node.
 
 ## Known Issues
 

README.md

@@ -0,0 +1 @@
+MS Annika 2.0 version 2.2.1

examples/data.zip

@@ -1 +1 @@
-MS Annika 2.0 version 1.2.0
+MS Annika 2.0 version 2.2.1