LC-MALDI analysis of HeLa and Gram-negative bacterium mixed digests for LFQ validation

Proteomic mixtures of HeLa and the Gram-negative bacterium Serratia proteamaculans (SePr) digests, with total protein amounts of 600 ng, were analyzed in triplicates. The set of mixtures was: SePr 500 ng and HeLa 100 ng, SePr 400 ng and HeLa 200 ng, SePr 200 ng and HeLa 400 ng, SePr 100 ng and HeLa 500 ng. This set allowed assessment of 1.25-, 2-, 2.5-, 4-, and 5-fold changes in protein abundance. 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 and Serratia proteamaculans proteomes. 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 Summary.txt, Protein Summary.txt files, and search database.