Protein Quantification in Mass Spectrometry-Based Proteomics
Creating a list of matrices of fragment ion intensities for all protei...
Protein quantification for a list of proteins
Protein annotation extraction
The MaxLFQ algorithm
Data filtering and normalization
Reading data from an input file
The MaxLFQ algorithm for protein quantification
The meanInt algorithm for protein quantification
A wrapper for the R implementation of the median polish algorithm
Plotting the underlying quantitative data for a protein
Data preprocessing for protein quantification
Long format to a wide format table using the MaxLFQ algorithm
Merging rows with identical values in a particular column in a table
The topN algorithm for protein quantification
An implementation of the MaxLFQ algorithm by Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160). In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.