Systematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics

Antimicrobial effects of peptides from fenugreek and ginger proteins using Fe3O4@PDA-MWCNT conjugated trypsin by improving enzyme stability & applications

Trypsin was immobilized onto a newly formulated nanocomposite (NC) comprising magnetic (Fe3O4) multiwalled carbon nanotubes (MWCNTs) anchored with polydopamine (PDA). The fabricated NC and the NC-bound trypsin were subjected to comprehensive characterization using various biophysical techniques including Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and fluorescence spectroscopy. The NC-bound trypsin exhibited significantly enhanced thermostability and increased tolerance to various organic solvents and denaturants. The enzymatic activity of trypsin was notably augmented through its coupling with the nano support, yielding an effectiveness factor (η) of 2.65. Fenugreek and ginger protein hydrolysates, prepared using both native and NC-bound enzyme, were evaluated for their antimicrobial activities. The analysis revealed that peptides generated by NC-bound trypsin showed higher antimicrobial activity (~ 10) in most cases compared to peptides obtained by using native trypsin. This strategy presents an innovative methodology for the production of potential biopeptides, with the prospect of their incorporation into pharmaceutical and therapeutic sectors through the utilization of NC-bound trypsin in protein hydrolysis.

Overview of in-capillary enzymatic reactions using capillary electrophoresis

This review summarizes the research that has recently been performed on in-capillary enzymatic reactions integrated with capillary electrophoresis. The manuscript is subdivided in homogeneous and heterogeneous approaches. The main homogeneous techniques are Electrophoretically Mediated Microanalysis, At-inlet and Transverse Diffusion of Laminar Flow Profiles. The main heterogeneous ones are Immobilized MicroEnzyme Reactors with enzymes grafted on either non-magnetic or magnetic particles. The overview covers the period from 2018 to early 2021. The applications range from drug discovery over natural products to food, beverage and pesticide analysis.

Ultrasonic-Based Filter Aided Sample Preparation as the General Method to Sample Preparation in Proteomics

We propose a new high-throughput ultrafast method for large-scale proteomics approaches by speeding up the classic filter aided sample preparation protocol, FASP, from overnight to 2.5 h. Thirty-six samples can be treated in 2.5 h, and the method is scalable to 96-well plate-based pipelines. After a modification of the FASP-tube, the steps of protein reduction, protein alkylation, and protein digestion of complex proteomes are done in just 5.25 min, each one under the effects of an ultrasonic field (7 cycles: 30 s on and 15 s off). The new method was compared to the standard overnight digestion FASP protocol, and no statistical differences were found for more than 92.4%, 92%, and 93.3% of the proteins identified by studying the proteome of E. coli, mouse brain, and mouse liver tissue samples, respectively. Furthermore, the successful relative label-free quantification of four spiked proteins in E. coli samples, BSA, β-lactoglobulin, α-casein, and α-lactalbumin, was achieved, using either the ultrasonic-based FASP protocol or the classic overnight one. The new US-FASP method matches the analytical minimalism rules as time, cost, sample requirement, reagent consumption, energy requirements, and production of waste products are reduced to a minimum while maintaining high sample throughput in a robust manner as all of the advantages of the filter aided sample preparation protocol are maintained.

Deep Intact Proteoform Characterization in Human Cell Lysate Using High-pH and Low-pH Reversed-Phase Liquid Chromatography

Post-translational modifications (PTMs) play critical roles in biological processes and have significant effects on the structures and dynamics of proteins. Top-down proteomics methods were developed for and applied to the study of intact proteins and their PTMs in human samples. However, the large dynamic range and complexity of human samples makes the study of human proteins challenging. To address these challenges, we developed a 2D pH RP/RPLC-MS/MS technique that fuses high-resolution separation and intact protein characterization to study the human proteins in HeLa cell lysate. Our results provide a deep coverage of soluble proteins in human cancer cells. Compared to 225 proteoforms from 124 proteins identified when 1D separation was used, 2778 proteoforms from 628 proteins were detected and characterized using our 2D separation method. Many proteoforms with critically functional PTMs including phosphorylation were characterized. Additionally, we present the first detection of intact human GcvH proteoforms with rare modifications such as octanoylation and lipoylation. Overall, the increase in the number of proteoforms identified using 2DLC separation is largely due to the reduction in sample complexity through improved separation resolution, which enables the detection of low-abundance PTM-modified proteoforms. We demonstrate here that 2D pH RP/RPLC is an effective technique to analyze complex protein samples using top-down proteomics.

Microscale Reversed-Phase Liquid Chromatography/Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Deep and Highly Sensitive Bottom-Up Proteomics: Identification of 7500 Proteins with Five Micrograms of an MCF7 Proteome Digest

Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has been well recognized for bottom-up proteomics. It has approached 4000-8000 protein identifications (IDs) from a human cell line, mouse brains, or Xenopus embryos via coupling with liquid chromatography (LC) prefractionation. However, at least 500 μg of complex proteome digests were required for the LC/CZE-MS/MS studies. This requirement of a large amount of initial peptide material impedes the application of CZE-MS/MS for deep bottom-up proteomics of mass-limited samples. In this work, we coupled microscale reversed-phase LC (μRPLC)-based peptide prefractionation to dynamic pH-junction-based CZE-MS/MS for deep bottom-up proteomics of the MCF7 breast cancer cell proteome starting with only 5 μg of peptides. The dynamic pH-junction-based CZE enabled a 500 nL sample injection from as low as a 1.5 μL peptide sample, using up to 33% of the available peptide material for an analysis. Two kinds of μRPLC prefractionation were investigated, C18 ZipTip and nanoflow RPLC. C18 ZipTip/CZE-MS/MS identified 4453 proteins from 5 μg of the MCF7 proteome digest and showed good qualitative and quantitative reproducibility. Nanoflow RPLC/CZE-MS/MS produced over 7500 protein IDs and nearly 60 000 peptide IDs from the 5 μg of MCF7 proteome digest. The nanoflow RPLC/CZE-MS/MS platform reduced the required amount of complex proteome digests for LC/CZE-MS/MS-based deep bottom-up proteomics by 2 orders of magnitude. Our work provides the proteomics community with a powerful tool for deep and highly sensitive proteomics.