Raw data files included in the 13553_STD_EAEHPM.zip file:

Quantification and PSM databases, including raw spectra:
decoy_psmlookup.sql
quant_lookup.sql
target_psmlookup.sql

Pipeline run files and QC reports:
pipeline_report.html
qc_full.html
qc_light.html
allplates
nr_spec_per_file
scans_per_plate

Processed data tables:
decoy_psmtable.txt
genes_table.txt
peptides_table.txt
proteins_table.txt
target_psmtable.txt

The file proteins_table.txt corresponds to the raw data which is later processed in "Processed data and analysis.xlsx".