TopDIA
TopDIA is the first software tool for top-down proteoform identification using TD-DIA-MS data. TopDIA generates pseudo non-multiplexed MS/MS spectra from TD-DIA-MS data by integrating algorithms for detecting and matching proteoform and fragment features.
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Code Availability:
TopDIA has been made available as part of TopPIC suite and can be downloaded from
https://github.com/toppic-suite/toppic-suite.
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Executables, manual, and tutorials:
You can download zipped executable files and find a manual and
tutorials of TopDIA at
https://www.toppic.org/.
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Evaluation Scripts:
Logistic regression model training and evaluation scripts are made available as a GitHub repository and are available at
https://github.com/ARBasharat/TopDIA_Evaluation_Scripts.
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Data:
The raw and mzML top-down MS data files of E. coli
used in the paper are available at RAW
and
mzML . The files are also available at the MassIVE
repository (ID: MSV000094407).
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Identification Results:
Proteoform identification results obtained for TD-DDA-MS and TD-DIA-MS E. coli data sets are available at:
link.
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Model Training Data:
Data used to train the logistic regrssion model is available at
link.
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Testing Data:
Data used to compare the performance of E. coli data generated using TD-DDA-MS and TD-DIA-MS is available at
link.