Effects of temperature on ultrasound-assisted tryptic protein digestion

RUPE-phospho: Rapid Ultrasound-Assisted Peptide-Identification-Enhanced Phosphoproteomics Workflow for Microscale Samples

Global phosphoproteome profiling can provide insights into cellular signaling and disease pathogenesis. To achieve comprehensive phosphoproteomic analyses with minute quantities of material, we developed a rapid and sensitive phosphoproteomics sample preparation strategy based on ultrasound. We found that ultrasonication-assisted digestion can significantly improve peptide identification by 20% due to the generation of longer peptides that can be detected by mass spectrometry. By integrating this rapid ultrasound-assisted peptide-identification-enhanced proteomic method (RUPE) with streamlined phosphopeptide enrichment steps, we established RUPE-phospho, a fast and efficient strategy to characterize protein phosphorylation in mass-limited samples. This approach dramatically reduces the sample loss and processing time: 24 samples can be processed in 3 h; 5325 phosphosites, 4549 phosphopeptides, and 1888 phosphoproteins were quantified from 5 μg of human embryonic kidney (HEK) 293T cell lysate. In addition, 9219 phosphosites were quantified from 1-2 mg of OCT-embedded mouse brain with 120 min streamlined RUPE-phospho workflow. RUPE-phospho facilitates phosphoproteome profiling for microscale samples and will provide a powerful tool for proteomics-driven precision medicine research.

Effect of Physical and Enzymatic Pre-Treatment on the Nutritional and Functional Properties of Fermented Beverages Enriched with Cricket Proteins

The aim of this study was to evaluate the effects of γ-irradiation (IR), ultrasound (US), and combined treatments of ultrasound followed by γ-irradiation (US-IR), ultrasound followed by enzymatic hydrolysis with and without centrifugation (US-E and US-EWC, respectively), and ultrasound followed by γ-irradiation and enzymatic hydrolysis (US-IRE), on the digestibility and the nutritional value of fermented beverages containing probiotics. Results showed that US (20 min), IR (3 kGy) and US-IR (tUS = 20 min, dose = 3 kGy) treatments raised protein solubility from 11.5 to 21.5, 24.3 and 29.9%, respectively. According to our results, these treatments were accompanied by the increased amount of total sulfhydryl groups, surface hydrophobicity and changes to the secondary structure of the proteins measured by Fourier-transform infrared spectroscopy (FTIR). Fermented probiotic beverages, non-enriched (C) and enriched with untreated (Cr) or treated cricket protein with combined treatments were also evaluated for their in vitro protein digestibility. Results showed that the soluble fraction of US-IRE fermented beverage had the highest digestibility (94%) as compared to the whole fermented tested beverages. The peptides profile demonstrated that US-IRE had a low proportion of high molecular weight (MW) peptides (0.7%) and the highest proportion of low MW peptides by over 80% as compared to the other treatments.

Effects of incubation temperature and acetonitrile amount on microwave-assisted tryptic digestion of proteins

The effects of incubation temperature and acetonitrile (ACN) amount on microwave-assisted tryptic digestion of horse skeletal muscle myoglobin (MYG) and bovine serum albumin (BSA) were investigated. Microwave-assisted tryptic digestion was performed on BSA or MYG solutions containing different amounts (0, 10, and 20%) of ACN for different times (10, 20, 30, 40, and 50 min) at different temperatures (25, 37, and 55 °C). Conventional overnight tryptic digestion was also conducted with gentle mixing at 37 °C for 16 h. Digested samples were analyzed using matrix-assisted laser desorption/ionization mass spectrometry. Similar sequence coverage (SC) values were obtained under most conditions except when the protein sample solutions were digested with 20% ACN at 55 °C, which provided the lowest SC for both MYG and BSA for all investigated digestion times. Considering the missed cleavage (MC) ratios for 50-min microwave-assisted digestion, the highest MC ratio, (i.e., lowest trypsin activity) was observed for the digestion condition of 20% ACN at 55 °C for both proteins, while the lowest MC ratio was observed with 0% ACN at 25 °C for MYG and with 0% ACN at 55 °C for BSA. Conventional overnight tryptic digestion at 37 °C provided more completely cleaved peptides than 50-min microwave-assisted tryptic digestion at the same temperature.

Perspectives on potentiating immunocapture-LC-MS for the bioanalysis of biotherapeutics and biomarkers

The integration of ligand-binding assay and LC-MS/MS (immunocapture-LC-MS) has unleashed the combined advantages of both powerful techniques for addressing the ever increasing bioanalytical challenges for biotherapeutics and biomarker assays. The highly specific, selective and sensitive characteristics of the immunocapture-LC-MS-based assays have enabled the determination of biotherapeutics and biomarkers in biomatrices with ease of method development, less requirements on key reagents as well as structural specificity for endogenous and engineered biomolecules. In addition, the versatile immunocapture-LC-MS technology has expanded into many challenging areas to enhance mechanistic studies of drug interactions with their targets. This paper intends to summarize our perspectives on enhancing the use of immunocapture-LC-MS in drug discovery and development for emerging new modalities.

Ultrasound promotes enzymatic reactions by acting on different targets: Enzymes, substrates and enzymatic reaction systems

With the extensive application of enzyme-catalyzed reactions in numerous fields, improving enzymatic efficiency has attracted wide attention for reducing operating costs and increasing output. There are three targets throughout enzymatic reactions: the enzyme, substrate, and mixed reaction system. Ultrasound has been known to accelerate enzymatic reactions by acting on different targets. It can modify both enzyme and substrate macromolecules, which is helpful for enhancing enzyme activity and product yields. The synergistic effect of ultrasound and enzymes is widely reported to increase catalytic rates. The present review discusses the positive effect induced by ultrasound throughout the enzymatic process, including ultrasonic modification of enzymes, ultrasound assisted immobilization, ultrasonic pretreatment of substrates, and ultrasound assisted enzymatic reactions.

Studying the effect of microwave heating on the digestion process and identification of proteins

The impact of microwave irradiation on the in-solution digestion processes and the detection limit of proteins are systematically studied. Kinetic processes of many peptides produced through the trypsin digestion of various proteins under microwave heating at 50°C were investigated with MALDI-MS. This study also examines the detection limits and digestion completeness of individual proteins under microwave heating at 50°C and at different time intervals (1, 5 and 30 min) using LC-MS. We conclude that if the peptides without missed cleavage dictate the detection limit, conventional digestion will lead to a better detection limit. The detection limit may not differ between the microwave and conventional heating if the peptides with missed cleavage sites and strong intensity are formed at the very early stage (i.e., less than 1 min) and are not further digested throughout the entire digestion process. The digestion of Escherichia coli lysate was compared under conventional and short time (microwave) conditions. The number of proteins identified under conventional heating exceeded that obtained from microwave heating over heating periods less than 5 min. The overall results show that the microwave-assisted digestion is not complete. Although the sequence coverage might be better, the detection limit might be worse than that under conventional heating.

A one-step preparation method of monolithic enzyme reactor for highly efficient sample preparation coupled to mass spectrometry-based proteomics studies

Mass spectrometry (MS) coupled to sample preparation and separation techniques has become a primary tool for proteomics studies. However, due to sample complexity, it is often challenging to achieve fast and efficient sample preparation prior to MS analysis. In recent decades, monolithic materials have been developed not only as chromatographic media, but also as efficient solid supports for immobilizing multiple types of affinity reagents. Herein, the N-acryloxysuccinimide-co-acrylamide-co-N,N'-methylenebisacrylamide (NAS-AAm-Bis) monolith was fabricated within silanized 200 μm i.d. fused-silica capillaries and was used as an immobilized enzyme reactor (IMER). The column was conjugated with trypsin/Lys-C and Lys-N enzymes to allow enzymatic digestions to occur while protein mixture was loaded onto the IMER column followed by MS-based proteomics analysis. Similar MS signal and protein sequence coverage were observed using protein standard bovine serum albumin (BSA) compared to in-solution digestion. Furthermore, mouse serum, yeast, and human cell lysate samples were also subjected to enzymatic digestion by both IMER (in seconds to minutes) and conventional in solution digestion (overnight) for comparison in large-scale proteomics studies. Comparable protein identification results obtained by the two methods highlighted the potential of employing NAS-based IMER column for fast and highly efficient sample preparation for MS analysis in proteomics studies.

Clarification of a peak at m/z 1634 from tryptically digested cytochrome c

A peptide peak at m/z 1634 in the mass spectrum of tryptically digested cytochrome c has been ambiguously assigned to either a peptide IFVQKCAQCHTVEK or a peptide CAQCHTVEK combined with a heme group (CAQCHTVEK + heme (Fe(III))). A comprehensive investigation was performed to clearly identify the origin of the peak. Tryptic digests of cytochrome c were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), liquid chromatography-tandem MS (LC-MS/MS), LC-ultraviolet (LC-UV), and MALDI Fourier transform-ion cyclotron resonance (FT-ICR) MS. The use of instruments with extremely high mass accuracy revealed the mass difference between the IFVQKCAQCHTVEK and the (CAQCHTVEK + heme (Fe(III))) ions. Fragmentation of the peptide associated with the unknown peak yielded a heme ion and other fragment ions originating from a (CAQCHTVEK + heme (Fe(III))) ion. Furthermore, an absorption peak at 395 nm confirmed the presence of a heme group in the unknown peptide. High mass accuracy analyses of MS and MS/MS spectra, in addition to three-dimensional UV contour mapping, showed that the peak at m/z 1634 is due to a (CAQCHTVEK + heme (Fe(III))) ion and not from protonated IFVQKCAQCHTVEK.