Relative quantification of proteins in MARC-145 cells during the PRRSV infection using a label-free methodology.
Description
The goal of this experiment was quantify the changes at the protein level during the infection of the PRRS virus (PRRSV) in MARC-145 cells (mexican strain) using label-free based data-independent acquisition (DIA) approach. This dataset contains all measurements given by the mass spectrometer. In the folder "peptide identification" are located all the * .csv files that contain the peptide sequences identified by mass spectrometry. There are 3 files for the control condition and another 3 files for the infected condition. In the * .xlsx file "messurments by mass spectrometry", are all identified proteins with their abundances. On the first sheet "TOTAL PROTEINS" are the raw intensities measured in the mass spectrometer for each detected protein, also we report anova, q-value, number of total and unique peptides. On the second sheet "ONLY ID BUT NOT QUANT" we filtered only the proteins which were not quantified, including those which have not unique peptides. On the third sheet, "EXCLUSIVE PROTEINS" are the proteins which are unique in a given condition. In this experiment we reported 2 proteins in the control stage (no infection). On the fourth sheet "QUANTIFIED PROTEINS" are all the proteins which could be quantified by the Hi3 method, described by Silva et al 2006 (Mol Cell Prot); in this section we calculated other values like -Log10(Anova), average Intensity, Log10(average Intensity), coefficients of variation (CV), positions in the dynamic range (ID´s), how many times the proteins were detected considering a triplicate (count), ratio (infected cells/no infected cells), and log2 (Ratio); all these values help in the development of quality control of the entire study. On the fifth sheet "UNCHANGED", we reported 699 proteins which not changed the abundance between infected and no infected stage. On the sixth sheet "UP", we reported 17 proteins which are up-regulated during the PRRSV infection; and finally on the seventh sheet "DOWN", we reported 19 proteins which are down-regulated during the PRRSV infection. Unchanged (699), up (17), down (19) regulated proteins were selected through a restrictive filter: a coefficient of variation (CV) ≤ 0.15, at least 2 peptides per protein, considering in those at least 1 unique peptide and ANOVA ≤ 0.05, and all proteins considered differentially expressed display at least a ratio of ±1.2 (expressed as a base 2 logarithm); it means that these proteins had at least ± 2.29- absolute fold change. For the realization of this experiment, we used a Synapt G2-Si mass spectrometer (Waters) in Ultra Definition Multiplexed-MS/MS (UDMSE) mode, and Progenesis QI for Proteomics software v3.0.3 (Waters) for the quantification.