pd_psm_input: Example Proteome Discoverer evidence file from the output of...
In Vitek-Lab/MSstatsPTM: Statistical Characterization of Post-translational Modifications
pd_psm_input R Documentation
Example Proteome Discoverer evidence file from the output of a label free experiment
Description
Experiment was performed by the Olsen lab and published on Nat. Commun.
(citation below).
Usage
pd_psm_input
Format
a data.table with 60 columns and 1657 rows, the output of PD
Details
Bekker-Jensen, D.B., Bernhardt, O.M., Hogrebe, A. et al. Rapid and
site-specific deep phosphoproteome profiling by data-independent acquisition
without the need for spectral libraries. Nat Commun 11, 787 (2020).
https://doi.org/10.1038/s41467-020-14609-1
The experiment was processed using Proteome Discoverer by the computational
proteomics team at Pfizer (Liang Xue and Pierre Jean).
The experiment did not contain a global profiling run, but we show an example
of extracting the unmodified peptides and using them in place of the
profiling run.
Examples
head(pd_psm_input)
Vitek-Lab/MSstatsPTM documentation built on April 21, 2024, 6:45 a.m.
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| pd_psm_input | R Documentation |
Example Proteome Discoverer evidence file from the output of a label free experiment
Description
Experiment was performed by the Olsen lab and published on Nat. Commun. (citation below).
Usage
pd_psm_input
Format
a data.table with 60 columns and 1657 rows, the output of PD
Details
Bekker-Jensen, D.B., Bernhardt, O.M., Hogrebe, A. et al. Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries. Nat Commun 11, 787 (2020). https://doi.org/10.1038/s41467-020-14609-1
The experiment was processed using Proteome Discoverer by the computational proteomics team at Pfizer (Liang Xue and Pierre Jean).
The experiment did not contain a global profiling run, but we show an example of extracting the unmodified peptides and using them in place of the profiling run.
Examples
head(pd_psm_input)
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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