Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus

Munday, Diane C.; Emmott, Edward; Surtees, Rebecca; Lardeau, Charles-Hugues; Wu, Weining; Duprex, W. Paul; Dove, Brian K.; Barr, John N.; Hiscox, Julian A.

LC-MS/MS analysis identified 606 and 534 proteins in the nuclear (supplemental Table 1 ) and cytoplasmic (supplemental Table 2 ) fractions, respectively. Of these, 561 and 520 proteins were identified and quantified in the nuclear and cytoplasmic fractions, respectively. All proteins were identified by two or more peptides. Mitochondrial proteins (74 proteins; supplemental Table 3 ) were present in the nuclear fraction, and these were removed from the final list of proteins assigned to the nuclear proteome (supplemental Table 4 ). The proteins classified as forming the cytoplasmic proteins are shown in supplemental Table 5 . A previous analysis of nuclear fractions obtained from A549 cells (prepared by a different method) also contained mitochondrial proteins, which were shown to be contaminants (33) . Five viral proteins were identified in both fractions (NS1, N, P, M, and M2-1 proteins), and one viral protein, F protein, was identified in the cytoplasmic fraction only (see supplemental Tables 6 and 7 for viral proteins found in the nuclear and cytoplasmic fractions, respectively).