PTPredict

set of programs implementing The OpenMS Proteomic Pipeline

Install

All systems
curl cmd.cat/PTPredict.sh
Debian Debian
apt-get install topp
Ubuntu
apt-get install topp
image/svg+xml Kali Linux
apt-get install topp
Fedora
dnf install openms
Windows (WSL2)
sudo apt-get update sudo apt-get install topp
Raspbian
apt-get install topp
Dockerfile
dockerfile.run/PTPredict

topp

set of programs implementing The OpenMS Proteomic Pipeline

TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of a set of numerous small applications that can be chained together to create analysis pipelines tailored for a specific problem. The applications make use of the libopenms library. Some examples of these applications are : - TOPPView: A viewer for mass spectrometry data. - TOPPAS: An assistant for GUI-driven TOPP workflow design. - DTAExtractor: Extracts spectra of an MS run file to several files in DTA format. - FileConverter: Converts between different MS file formats. - FileFilter: Extracts or manipulates portions of data from peak, feature or consensus feature files. - SpectraMerger: Merges spectra from an LC/MS map, either by precursor or by RT blocks. - BaselineFilter: Removes the baseline from profile spectra using a top-hat filter. - InternalCalibration: Applies an internal calibration. - PTModel: Trains a model for the prediction of proteotypic peptides from a training set. - RTPredict: Predicts retention times for peptides using a model trained by RTModel. - ExecutePipeline: Executes workflows created by TOPPAS.

openms

package for LC/MS data management and analysis

OpenMS is a package for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions. TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of a set of numerous small applications that can be chained together to create analysis pipelines tailored for a specific problem. This package is a metapackage that depends on both the libopenms library package (libOpenMS and libOpenMS_GUI) and the OpenMS Proteomic Pipeline (topp) package.