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:

##### PARAMETERS #####

SPECTRA_FILE = "20220215_Eclipse_LC6_PepMap50cm-cartridge_mainlib_DSSO_3CV_stepHCD_OT_001.mgf"
CSMS_FILE = "CSMs_unfiltered.xlsx"
DOUBLETS_FILE = "CrosslinkDoublets.txt"
MODIFICATIONS = \
    {"Oxidation": [15.994915],
     "Carbamidomethyl": [57.021464],
     "DSSO": [54.01056,  85.98264, 103.99320]}
ION_TYPES = ("b", "y")
MAX_CHARGE = 4
MATCH_TOLERANCE = 0.02
DOUBLET_IDENTIFICATION_MODE = "All"
# DOUBLET_IDENTIFICATION_MODE = "Evidence"
# DOUBLET_IDENTIFICATION_MODE = "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:

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

MS Annika: A New Cross-Linking Search Engine
Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, and Viktoria Dorfer
Journal of Proteome Research 2021 20 (5), 2560-2569
DOI: 10.1021/acs.jproteome.0c01000

License

Contact

[email protected]

hgb-bin-proteomics / msannika_csm_annotation Goto Github PK