Twelve LC-MALDI runs of 500 ng HeLa protein digest standard

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 *.fasta. Samples were analyzed in three batches, each with four independent LC-MALDI runs of 500 ng of HeLa protein digest standard. Batch 1 includes runs A, B, C, D. Batch 2 includes runs E, F, G, H. Batch 3 includes runs I, J, K, L.