Quantitative Proteomic Analysis of MARC-145 Cells Infected with a Mexican Porcine Reproductive and Respiratory Syndrome Virus Strain Using a Label-Free Based DIA approach

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is an infectious disease characterized by severe reproductive failure in sows, acute respiratory disorders in growing pigs, and high mortality in piglets. The causative agent of this syndrome is the PRRS virus (PRRSV), an RNA virus belonging to the Arteriviridae family. To date, several quantitative approaches of proteomics have been applied to analyze the gene expression profiles during PRRSV infection in PAMs and MARC-145 cells, and few proteins have been consistent among independent studies, probably due to the differences in the levels of virulence of different PRRSV strains used and/or due to analytical conditions. In this study, total proteins isolated from noninfected and infected MARC-145 cells with a Mexican PRRSV strain were relatively quantified using label-free based DIA approach in combination with ion-mobility separation. As a result, 1456 quantified proteins were found to be shared between the control and infected samples. Afterward, these proteins were filtered, and 699 of them were considered without change. Also, 17 proteins were up-regulated and 19 proteins were down-regulated during the PRSSV infection. Bioinformatic analysis revealed that many of the differentially expressed proteins are involved in processes like antigen processing, presentation of antigens, response to viruses, response to IFNs, and innate immune response, among others. The present work is the first one which provides a detailed proteomic analysis through label-free based DIA approach in MARC-145 cells during the infection with a Mexican PRRSV strain.

The Proteome Profile of Olfactory Ecto-Mesenchymal Stem Cells-Derived from Patients with Familial Alzheimer’s Disease Reveals New Insights for AD Study

“…Subsequently, they were rinsed with 50 μL of 0.5 M NaCl and centrifuged again (twice); finally, the sample was desalted in a C18 resin column and stored at −80 °C until further use. Digestion of the samples was according to the FASP protocol described by Wiśniewski et al [ 184 ] and modified by the LaNSE CINVESTAV proteomics team [ 185 ].…”

An Initial Proteomic Analysis of Biogas-Related Metabolism of Euryarchaeota Consortia in Sediments from the Santiago River, México

“…The LC-MS analytical method was applied according to Ríos-Castro et al with some modifications [ 33 ]. Briefly, 3.5 µL of tryptic peptides was loaded and separated on an HSS T3 C18 column (Waters, Milford, MA, USA; 75 μm × 150 mm, 100 Å pore size, 1.8 μm particle size) using an ACQUITY M-Class UPLC with the following mobile phases: A, 0.1% FA in water; and B, 0.1% FA in ACN.…”

Expression Profiles of Kidney Mitochondrial Proteome during the Progression of the Unilateral Ureteral Obstruction: Focus on Energy Metabolism Adaptions

“…Peptides were injected into the mass spectrometer Synapt G2–Si (Waters, Milford, MA, USA) in MS E mode to calculate the area under the curve (AUC) of the total ion chromatogram (TIC), to normalize the injection prior to LC–MS analysis and, therefore, inject a comparable sample quantity for both conditions [ 23 ]. Afterwards, peptides in each sample were loaded and separated on an HSS T3 C18 column; 75 μm × 150 mm, 100 Å pore size, 1.8 μm particle size, using an UPLC ACQUITY M–Class with mobile phase A (0.1% formic acid in H 2 O) and mobile phase B (0.1% formic acid in acetonitrile) under the following gradient: 0 min 7% B, 121.49 min 40% B, 123.15 to 126.46 min 85% B, 129 to 130 min 7% B, at a flow of 400 nL·min –1 and 45 °C [ 23 ]. The spectra data were acquired in the mass spectrometer using nanoelectrospray ionization (nanoESI) and ion mobility separation (IMS) using the data–independent acquisition (DIA) approach through HDMS E mode.…”