README.md
In chrismckennan/MSeQUiP: Quantifying uncertainty in peptide-spectrum matches
MSeQUiP
Identify peptide-spectrum matches (PSMs) from LC-MS/MS data using the method described in https://arxiv.org/abs/2110.07818. The main function is , which uses described in to infer PSMs.
Functions
The main functions are:
PerformSearch
Use spectral libraries and our Bayes factor scoring function to infer PSMs.
Deisotope
Use our novel MS/MS deisotoping and charge assignment algorithm to clean MS/MS spectra.
SimulateDataPaper
Simulate realistic LC-MS/MS data using the method described in https://arxiv.org/abs/2110.07818.
AnalyzeSimulatedData
Analyze the above simulated.
Reproduce simulation results
To reproduce simulation results from https://arxiv.org/abs/2110.07818:
1) Download the data from https://drive.google.com/file/d/1Iz6WSTIQV-8nj5qPIKyrGv7NkVTW5YI1/view?usp=sharing
2) Unzip the folder and follow the instructions in Simulations.Rmd
chrismckennan/MSeQUiP documentation built on Dec. 19, 2021, 4:01 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
MSeQUiP
Identify peptide-spectrum matches (PSMs) from LC-MS/MS data using the method described in https://arxiv.org/abs/2110.07818. The main function is , which uses described in to infer PSMs.
Functions
The main functions are:
PerformSearch
Use spectral libraries and our Bayes factor scoring function to infer PSMs.
Deisotope
Use our novel MS/MS deisotoping and charge assignment algorithm to clean MS/MS spectra.
SimulateDataPaper
Simulate realistic LC-MS/MS data using the method described in https://arxiv.org/abs/2110.07818.
AnalyzeSimulatedData
Analyze the above simulated.
Reproduce simulation results
To reproduce simulation results from https://arxiv.org/abs/2110.07818: 1) Download the data from https://drive.google.com/file/d/1Iz6WSTIQV-8nj5qPIKyrGv7NkVTW5YI1/view?usp=sharing 2) Unzip the folder and follow the instructions in Simulations.Rmd
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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