pyOpenMS

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Introduction

Introduction
Background

Getting started

Installation
Import pyopenms
Getting help
First look at data

Mass Spectrometry Concepts

MS Data
Chemistry
Peptides and Proteins
Oligonucleotides: RNA
Fragment spectrum generation
Spectrum alignment
Digestion
Identification Data
Quantitative Data

OpenMS Algorithms

Parameter Handling
Algorithms
Smoothing
Centroiding
Spectrum normalization
Charge and Isotope Deconvolution
Feature Detection
Map Alignment
Feature Linking
Peptide Search
Chromagraphic Analysis
Quality Control
Mass Decomposition
Export files for GNPS

Example Workflows

Identification by Accurate Mass
Untargeted Metabolomics Pre-Processing

How to contribute

Contribute

Advanced Topics

Reading Raw MS data
Other MS data formats
mzML files
Export to pandas DataFrame
Query MSExperiment with MassQL
Memory management
pyOpenMS in R
Build from source
Wrapping Workflow and wrapping new Classes
Interactive plots
Interfacing with ML libraries

Full API documentation

Full API documentation

Support

Support
Frequently Asked Questions

pyOpenMS

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PeakMap
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PeakMap

pyopenms.PeakMap: alias of pyopenms.dataframes.MSExperimentDF

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