msannika_csm_annotation

Calculates Intensities of Cross-linked Peptides from MS Annika CSMs.

https://github.com/hgb-bin-proteomics/msannika_csm_annotation

Science Score: 65.0%

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Keywords

annotation cross-linking crosslinker crosslinking doublet-ions fragment-ions mass mass-spectrometry ms2 ms3 proteomics python spectrometry tandem-ms xlms

Last synced: 6 months ago · JSON representation ·

Repository

Calculates Intensities of Cross-linked Peptides from MS Annika CSMs.

Basic Info

Host: GitHub
Owner: hgb-bin-proteomics
License: mit
Language: Python
Default Branch: master
Homepage:
Size: 35.2 KB

Statistics

Stars: 1
Watchers: 3
Forks: 0
Open Issues: 1
Releases: 2

Topics

annotation cross-linking crosslinker crosslinking doublet-ions fragment-ions mass mass-spectrometry ms2 ms3 proteomics python spectrometry tandem-ms xlms

Created almost 3 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

MSAnnika CSM Annotation

Calculates fragment intensities and doublet intensities of cross-linked peptides from MS Annika CSMs.

Usage

Install requirements: pip install -r requirements.txt
Export MS Annika CSMs from Proteome Discoverer to Microsoft Excel format. Filter out decoys beforehand. Optionally also filter out low confidence CSMs.
[Optional] Export MS Annika Crosslink Doublets to text (tab seperated) if you want to annotate doublet peaks.
Convert any RAW files to *.mgf format.
Set your desired parameters in get_intensities.py.
Run python get_intensities.py.
If the script successfully finishes, there should be a new Excel file including intensities and annotations.

Parameters

The following parameters should be set inside the script:

```python

PARAMETERS

SPECTRAFILE = "20220215EclipseLC6PepMap50cm-cartridgemainlibDSSO3CVstepHCDOT001.mgf" CSMSFILE = "CSMsunfiltered.xlsx" DOUBLETSFILE = "CrosslinkDoublets.txt" MODIFICATIONS = \ {"Oxidation": [15.994915], "Carbamidomethyl": [57.021464], "DSSO": [54.01056, 85.98264, 103.99320]} IONTYPES = ("b", "y") MAXCHARGE = 4 MATCHTOLERANCE = 0.02 DOUBLETIDENTIFICATIONMODE = "All"

DOUBLETIDENTIFICATIONMODE = "Evidence"

DOUBLETIDENTIFICATIONMODE = "Indication"

```

The DOUBLETS_FILE parameter is optional, if a file is provided the doublet intensities will also be calculated, otherwise leave the field blank DOUBLETS_FILE = None and doublets will not be annotated and no doublet intensities will be calculated. DOUBLET_IDENTIFICATION_MODE can either be "All" which means all doublets will be considered or "Evidence" which means only doublets identified by MS Annika in evidence mode will be considered, or "Indication" which means only doublets identified by MS Annika in indication mode will be considered.

Known Issues

List of known issues

Citing

If you are using the MS Annika CSM Annotation script please cite: MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity Micha J. Birklbauer, Manuel Matzinger, Fränze Müller, Karl Mechtler, and Viktoria Dorfer Journal of Proteome Research 2023 22 (9), 3009-3021 DOI: 10.1021/acs.jproteome.3c00325

If you are using MS Annika please cite as described here.

License

Contact

micha.birklbauer@fh-hagenberg.at

Owner

Name: FHOOE Hagenberg Bioinformatics/Proteomics Research Group
Login: hgb-bin-proteomics
Kind: organization
Location: Austria

Website: https://bioinformatics.fh-hagenberg.at/
Repositories: 3
Profile: https://github.com/hgb-bin-proteomics

Bioinformatics/Proteomics Research Group of the FH OOE Hagenberg

Citation (CITATION.cff)

cff-version: 1.2.0
preferred-citation:
  type: article
  authors:
  - family-names: "Birklbauer"
    given-names: "Micha J."
    orcid: "https://orcid.org/0009-0005-1051-179X"
  - family-names: "Matzinger"
    given-names: "Manuel"
    orcid: "https://orcid.org/0000-0002-9765-7951"
  - family-names: "Müller"
    given-names: "Fränze"
    orcid: "https://orcid.org/0000-0003-3764-3547"
  - family-names: "Mechtler"
    given-names: "Karl"
    orcid: "https://orcid.org/0000-0002-3392-9946"
  - family-names: "Dorfer"
    given-names: "Viktoria"
    orcid: "https://orcid.org/0000-0002-5332-5701"
  doi: "10.1021/acs.jproteome.3c00325"
  journal: "Journal of Proteome Research"
  month: 9
  start: 3009
  end: 3021
  title: "MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity"
  issue: 9
  volume: 22
  year: 2023

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