Description Details Author(s) References
The package apmsWAPP provides a complete workflow for the analysis of AP-MS data, based on replicate single-bait purifications including negative controls.
It comprises the three main parts of pre-processing, scoring and postprocessing of interaction proteins:
For pre-processing, five different normalization methods and a filtering procedure is provided.
For scoring protein-protein-interactions, either the method of SAINT or a two-stage-poisson model (TSPM) adapted to AP-MS data can be chosen.
For postprocessing, the user can choose between the permutation-based approach of Westfall&Young (applicable to both, SAINT and TSPM) and the adjustment procedure of Benjamini-Hochberg (applicable to TSPM).
Postprocessing results in the generation of p-values for each interaction candidate, allowing to control the number of false-positive interactions.
Package: | apmsWAPP |
Type: | Package |
Version: | 1.0 |
Date: | 2013-03-14 |
License: | LGPL-3 |
The two main function calls are: saint_permF
(framework based on SAINT) and tspm_apms
(framework based on TSPM).
Note: saint_permF
can only be executed in a linux environment and SAINT must be installed accordingly.
tspm_apms
is applicable in a windows and a linux environment.
Martina Fischer (fischerm@rki.de)
Fischer M, Zilkenat S, Gerlach R, Wagner S, Renard BY. Pre- and Post-Processing Workflow for Affinity Purification Mass Spectrometry Data. Journal of Proteome Research 2014.
Choi H, Larsen B, Lin Z-Y, et al. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nature Methods 2011.
Auer PL, Doerge RW. A two-stage Poisson model for testing RNA-Seq data. Statistical Applications in Genetics and Molecular Biology 2011.
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