IO: io

Read proteomics data from various search engines and file formats into AnnData objects. These functions leverage the protdata package to parse search engine outputs and standardize proteomics data for analysis.

Search Engine Outputs

Read proteomics data from common search engine outputs (MaxQuant, DIA-NN, FragPipe).

io.read_maxquant	Read MaxQuant proteinGroups.txt file into an AnnData object.
io.read_diann	Read DIA-NN report.tsv file into an AnnData object.
io.read_fragpipe	Read FragPipe combined_protein.tsv file into an AnnData object.

Other Formats

Read data from other subcellular proteomics analysis tools.

io.read_prolocdata

Read a prolocdata file and return an AnnData object.