| create_protein_list | Creating a list of matrices of fragment ion intensities for all proteins | 
| create_protein_table | Protein quantification for a list of proteins | 
| extract_annotation | Protein annotation extraction | 
| fast_MaxLFQ | The MaxLFQ algorithm | 
| fast_preprocess | Data filtering and normalization | 
| fast_read | Reading data from an input file | 
| maxLFQ | The MaxLFQ algorithm for protein quantification | 
| meanInt | The meanInt algorithm for protein quantification | 
| median_polish | A wrapper for the R implementation of the median polish algorithm | 
| plot_protein | Plotting the underlying quantitative data for a protein | 
| preprocess | Data preprocessing for protein quantification | 
| process_long_format | Long format to a wide format table using the MaxLFQ algorithm | 
| process_wide_format | Merging rows with identical values in a particular column in a table | 
| spikeins | An example dataset of 12 spike-in proteins | 
| topN | The topN algorithm for protein quantification |