Bottom‐up proteome analysis of E. coli using capillary zone electrophoresis‐tandem mass spectrometry with an electrokinetic sheath‐flow electrospray interface

The Escherichia coli proteome was digested with trypsin and fractionated using SPE on a C18 SPE column. Seven fractions were collected and analyzed by CZE‐ESI‐MS/MS. The separation was performed in a 60‐cm‐long linear polyacrylamide‐coated capillary with a 0.1% v/v formic acid separation buffer. An electrokinetic sheath‐flow electrospray interface was used to couple the separation capillary with an Orbitrap‐Velos operating in higher‐energy collisional dissociation mode. Each CZE‐ESI‐MS/MS run lasted 50 min and total MS time was 350 min. A total of 23 706 peptide spectra matches, 4902 peptide IDs, and 871 protein group IDs were generated using MASCOT with false discovery rate less than 1% on the peptide level. The total mass spectrometer analysis time was less than 6 h, the sample identification rate (145 proteins/h) was more than two times higher than previous studies of the E. coli proteome, and the amount of sample consumed (<1 μg) was roughly fourfold less than previous studies. These results demonstrate that CZE is a useful tool for the bottom‐up analysis of prokaryote proteomes.     

Systematic research on the pretreatment of peptides for quantitative proteomics using a C18 microcolumn

Reversed phase microcolumns have been widely used for peptide pretreatment to desalt and remove interferences before tandem LC–MS in proteomics studies. However, few studies have characterized the effects of experimental parameters as well as column characteristics on the composition of identified peptides. In this study, several parameters including the concentration of ACN in washing buffer, the microcolumn's purification effect, the peptide recovery rate, and the dynamic‐binding capacity were characterized in detail, based upon stable isotope labeling by amino acids in a cell culture quantitative approach. The results showed that peptide losses can be reduced with low ACN concentration in washing buffers resulting in a recovery rate of approximately 82%. Furthermore, the effects of ACN concentration and loading amount on the properties of identified peptides were also evaluated. We found that the dynamic‐binding capacity of the column was approximately 26 μg. With increased loading amounts, more hydrophilic peptides were replaced by hydrophobic peptides.     

INPPO Actions and Recognition as a Driving Force for Progress in Plant Proteomics: Change of Guard,INPPO Update,and Upcoming Activities

The International Plant Proteomics Organization (INPPO) is a non‐profit organization whose members are scientists involved or interested in plant proteomics. Since the publication of the first INPPO highlights in 2012, continued progress on many of the organization's mandates/goals has been achieved. Two major events are emphasized in this second INPPO highlights. First, the change of guard at the top, passing of the baton from Dominique Job, INPPO founding President to Ganesh Kumar Agrawal as the incoming President. Ganesh K. Agrawal, along with Dominique Job and Randeep Rakwal initiated the INPPO. Second, the most recent INPPO achievements and future targets, mainly the organization of first the INPPO World Congress in 2014, tentatively planned for Hamburg (Germany), are mentioned.     

Differential label‐free quantitative proteomic analysis of avian eggshell matrix and uterine fluid proteins associated with eggshell mechanical property

Eggshell strength is a crucial economic trait for table egg production. During the process of eggshell formation, uncalcified eggs are bathed in uterine fluid that plays regulatory roles in eggshell calcification. In this study, a label‐free MS‐based protein quantification technology was used to detect differences in protein abundance between eggshell matrix from strong and weak eggs (shell matrix protein from strong eggshells and shell matrix protein from weak eggshells) and between the corresponding uterine fluids bathing strong and weak eggs (uterine fluid bathing strong eggs and uterine fluid bathing weak eggs) in a chicken population. Here, we reported the first global proteomic analysis of uterine fluid. A total of 577 and 466 proteins were identified in uterine fluid and eggshell matrix, respectively. Of 447 identified proteins in uterine fluid bathing strong eggs, up to 357 (80%) proteins were in common with proteins in uterine fluid bathing weak eggs. Similarly, up to 83% (328/396) of the proteins in shell matrix protein from strong eggshells were in common with the proteins in shell matrix protein from weak eggshells. The large amount of common proteins indicated that the difference in protein abundance should play essential roles in influencing eggshell strength. Ultimately, 15 proteins mainly relating to eggshell matrix specific proteins, calcium binding and transportation, protein folding and sorting, bone development or diseases, and thyroid hormone activity were considered to have closer association with the formation of strong eggshell.     

Effect of Edge Rounding on the Extinction Properties of Hollow Metal Nanoparticles

The optical responses of metal nanoparticles induced by subtle variations in geometry, especially by the rounding of the edges and corners, have generated great interest at present due to the requirement of fabricating refined structures of metal nanoparticles and theoretical simulations of the real particles. We study the effect of both inner and outer edge rounding on the optical properties of gold nanobox and gold nanobox dimer with small interparticle distances by using the discrete dipole approximation method. The shift of extinction peaks, the electric field distribution, and the variation of refractive index sensitivities by changing the curvature of the inner and outer edges of gold nanobox are investigated. We demonstrate that the optical properties of nanobox are more sensitive to the outer edge rounding than the inner edge rounding. By edge rounding of two very close gold nanoboxes, the blue shift of the dipolar and the quadrupolar plasmonic resonances of nanobox dimer are shown. Comparing with the inner edge rounding of nanobox dimer, we find that rounding of the outer edges causes the larger shift of the quadrupolar mode and approximate shift of the dipole mode.     

Plasmonic Spectral Detection of Carcinoembryonic Antigen by Preventing the Direct Binding of Rhodamine 6G with Au Nanoparticles

Carcinoembryonic antigen (CEA) was used as a separator to prevent the Rhodamine 6G (R6G)-induced aggregation of colloidal gold nanoparticles. The destroyed aggregation has been monitored by measuring the absorption and resonance light scattering peaks corresponding to the longitudinal surface plasmon resonance (SPR) of the chain-like aggregated gold nanoparticles (AuNPs). It was found that the pre-adding of CEA with different concentrations to the gold colloids before mixing them with R6G could lead to the longitudinal SPR peak decrease and blue shift. By analysing the intensity changing and wavelength shifting of the absorption spectra, CEA could be detected in a linear range from 0.2 to 4 ng/mL, and the limit of detection reaches to 0.1 ng/mL. The sensitivity of the CEA concentration dependent shifting and quenching of the plasmonic absorption and scattering corresponding to the AuNPs aggregation presents a well potential application of biologic spectral sensing.