LC-MALDI analysis of HeLa protein digest standard for LFQ validation

Data were acquired using a TOF/TOF 5800 System (SCIEX) instrument operated in positive ion mode. The Protein Pilot 5.0.1 software (SCIEX) with the Paragon algorithm in thorough mode, was used for the MS/MS spectra search against the Homo sapiens proteome. The database also incorporated a list of common contaminants and decoy sequences generated with DecoyPYrat. The dataset comprises the following files: search results *.group, peak lists *.mgf, search results *.mzid, Distinct Petide Sumary.txt, Protein Summary.txt files, and search database. Hela digests were analyzed in triplicate at four different loads: 100 ng, 200 ng, 400 ng, and 800 ng.