Additional file 1:

Mass spectrometry traces. LC/MS/MS data for selected tryptic and chymotryptic peptides of low molecular mass products isolated from purified SFV virions. Data are presented for the following peptides: SLSFLSATEPR, TFDSNAER, SLSFL, SLSFLV and SLSFF. A. Primary FTMS mass spectra. B. Output from MASCOT software showing MS/MS fragmentation spectra and matched peptide sequences. Peptide assignments were based on a combination of the following criteria: (i) The mass error should be less than 3 ppm. (ii) A check of the primary FTMS data should confirm that the charge state of the molecular ion determined by the THERMO software is correct and consistent with the actual charge state of the ion that was searched by MASCOT. (iii) The MS/MS data (i.e. peptide sequence data) should be of good quality and show good signal-to-noise. The MASCOT-assigned ions should be prominent and generally the main ions accounted for in the MS/MS spectrum (not noise peaks). Mass errors for the ions in the MS/MS data should mostly be within 0.3 Da. Assigned ions in the MS/MS ion-trap data are frequently relatively minor peaks, but they should still have a reasonable signal-to-noise ratio, such as 5:1. (iv) The MASCOT score should usually be ≥ 20. However, the score for a given peptide is proportional to the number of fragment ions observed and assigned in the MS/MS data. Thus, for small peptides, such as SLSFL and SLSFF, the MASCOT score may be less than 20, provided the quality of the MS/MS data is still relatively good. (v) The 'expect' value should generally be ≤ 0.0001. However, once again, for small peptides expect values ≤ 0.01 may be acceptable, since the expect values also depend on peptide length.

Format: PDF Size: 1.9MB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 2:

Immunofluorescence of SFV-infected cells showing location of 6K and TF proteins. Green fluorescence indicates Abs binding to target peptides. Cell nuclei are stained blue. (A) Ab-TF-C – Ab to C-term of TF. (B) Ab-6KTF-N – Ab to common N-term of 6K and TF. (C) Anti-SFV Ab. Cells fixed in acetone are permeabilized, allowing intracellular Ab staining. Cells fixed in 4% PFA are not permeabilized, thus only allowing Abs to bind to peptides at the cell surface. Cells are infected with WT SFV4 virus (WT), the TF knockout mutant (TF^-), or are non-infected controls. TF^- also serves as an additional control for Ab-TF-C.

Format: JPEG Size: 1.9MB Download file