No abstract

Fig. S1. Gradient improvement for high pH SCX enrichment.A) Workflow of high pH SCX enrichment (1). LN229 cells were lysed in 8M urea and digested with trypsin. From 1 mg of protein, five fractions are produced by the SCX procedure and were subsequently run on a Q Exactive Plus MS. The data was searched on Proteome Discoverer 2.2 and methyl peptides were subject to a strict 1% methyl FDR. The number of PSMs for two gradients tested is shown in the table in E). B) Density plots of PSM retention times for methyl and nonmethyl PSMs run on the "Long" SCX gradient used from Wang et al.. PSMs from all 5 fractions were combined and their retention times plotted. The average density of nonmethyl PSMs and methyl PSMs was 275 PSM / min and 15 PSMs / min, respectively. C) Original "Long" gradient and a new proposed "Short" gradient for SCX. Wang et al. did not collect spectra for the first 20 min during sample loading, but because we found that methyl PSMs were eluting during this sample loading phase, we did collect spectra during this phase of the LC gradient. D) Density plot of methyl PSM retention time for methyl PSMs captured by the "Long" and "Short" SCX gradients. PSMs from all 5 fractions were combined and their retention times plotted for each gradient. The average density of "Long" and "Short" gradient methyl PSMs was 15 PSM / min and 19 PSMs / min, respectively. E) Summary of spectra identified by each gradient. Each of the five SCX fractions are shown individually. The numbers of methyl and nonmethyl PSMs were used to calculate the percent enrichment for each fraction. The number of MMA, Kme1, DMA, Kme2, PSMs, and mixed methyl PSMs are shown. Mixed PSMs contained a mixture of methyl marks on the same peptide (e.g.,MMA and DMA). The percolator q-value cutoff used to estimate the methyl FDR is also shown for each technique.

A systematic study of the protein corona's effect on nanoparticle–biomembrane electrostatic interactions. Nanoparticle adhesion and membrane integrity upon interaction were compared between plasma membranes and biomimetic membranes.