Selective extraction of peptides in acidic human plasma by porous silica nanoparticles for peptidome analysis with 2-D LC-MS/MS

Deciphering the protein digestion of meat products for the elderly by in vitro food oral processing and gastric dynamic digestion, peptidome analysis and modeling

The elderly population will increase sharply in the future, along with an emerging range of specific nutritional needs that include adapted food. We aimed to develop a workflow to study the fate of a food, objectify the bioavailability of nutrients in the case of the digestive physiology of the elderly, and model the fate of proteins in the stomach. Pork frankfurters were subjected to in vitro normal and deficient mastication and gastric digestion, mimicking adult and elderly food oral and digestive processing. Swallowable food boluses were characterized for granulometric and rheological properties. Biochemical analyses were conducted on the bolus and on the digesta. Macronutrients, label-free peptide quantification and identification were performed, and modeling was applied to protein digestion kinetics. After deficient mastication, the food bolus was harder with more large particles, lower free iron release and more protein oxidation. The amount of peptides released in the stomach progressively increased, but to a lower extent for the elderly digestive condition and irrespective of masticatory efficiency. 592 peptides were identified from 67 proteins. Different trajectories were observed for adult and elderly digestive conditions, and two groups of meat proteins were identified based on the rate of hydrolysis. Designing suitable foods requires in vitro tools to evaluate the possible benefit for the elderly. Besides the well-known notion of Food Oral Processing (FOP), our work broadens the concept by extending oral activity to digestion when working in a nutritional context. This new concept is named Food Oral and Digestive Processing, FODP.

High Anti-Interfering Profiling of Endogenous Glycopeptides for Human Plasma by the Dual-Hydrophilic Metal-Organic Framework

Glycopeptidome profiling provides large-scale information about the glycosylation level of endogenous peptides, reflecting the dynamic processes of disease occurrences and developments. However, endogenous glycopeptides are usually submerged in complex fluids containing a wide variety of interference molecules, such as high concentration proteins, nonglycopeptides, and salts, which confounds attempts to identify glycopeptidome. Here, a dual-hydrophilic metal-organic framework is developed to selectively capture endogenous glycopeptides in complex biological fluid. The hydrophilic matrix material provides specific selectivity toward glycopeptides, while the deliberate surface regulation using hydrophilic species enhances its interaction with glycopeptides. This hydrophilic probe presents an extremely high performance in anti-interfering enrichment of glycopeptides from mimic complex samples, even when the molar ratio of immunoglobulin G versus bovine serum albumin was up to about 1:5000. More excitingly, in the practical application of glycopeptidome analysis, a total of 380 endogenous N-glycopeptides with 180 unique N-glycopeptide sites were identified from human plasma. This strategy is expected to broaden the application of dual-hydrophilic MOF-based materials, especially in dealing with the challenges of extremely complex biological samples.

Mixed-mode ion exchange-based integrated proteomics technology for fast and deep plasma proteome profiling

Plasma proteome profiling by LC-MS based proteomics has drawn great attention recently for biomarker discovery from blood liquid biopsy. Due to standard multi-step sample preparation could potentially cause plasma protein degradation and analysis variation, integrated proteomics sample preparation technologies became promising solution towards this end. Here, we developed a fully integrated proteomics sample preparation technology for both fast and deep plasma proteome profiling under its native pH. All the sample preparation steps, including protein digestion and two-dimensional fractionation by both mixed-mode ion exchange and high-pH reversed phase mechanism were integrated into one spintip device for the first time. The mixed-mode ion exchange beads design achieved the sample loading at neutral pH and protein digestion within 30 min. Potential sample loss and protein degradation by pH changing could be voided. 1 μL of plasma sample with depletion of high abundant proteins was processed by the developed technology with 12 equally distributed fractions and analyzed with 12 h of LC-MS gradient time, resulting in the identification of 862 proteins. The combination of the Mixed-mode-SISPROT and data-independent MS method achieved fast plasma proteome profiling in 2 h with high identification overlap and quantification precision for a proof-of-concept study of plasma samples from 5 healthy donors. We expect that the Mixed-mode-SISPROT become a generally applicable sample preparation technology for clinical oriented plasma proteome profiling.

Organosilica hybrid nanomaterials with a high organic content: syntheses and applications of silsesquioxanes

Organic-inorganic hybrid materials garner properties from their organic and inorganic matrices as well as synergistic features, and therefore have recently attracted much attention at the nanoscale. Non-porous organosilica hybrid nanomaterials with a high organic content such as silsesquioxanes (R-SiO_1.5, with R organic groups) and bridged silsesquioxanes (O_1.5Si-R-SiO_1.5) are especially attractive hybrids since they provide 20 to 80 weight percent of organic functional groups in addition to the known chemistry and stability of silica. In the organosilica family, silsesquioxanes (R-SiO_1.5) stand between silicas (SiO₂) and silicones (R₂SiO), and are variously called organosilicas, ormosil (organically-modified silica), polysilsesquioxanes and silica hybrids. Herein, we comprehensively review non-porous silsesquioxane and bridged silsesquioxane nanomaterials and their applications in nanomedicine, electro-optics, and catalysis.

Separation/Preconcentration Techniques for Rare Earth Elements Analysis

The main aim of this chapter exactly characterizes the contribution. The analytical chemistry of the rare earth elements (REEs) very often is highly complicated and the determination of a specific element is impossible without a sample pre-concentration. Sample preparation can be carried out either by separation of the REEs from the matrix or by concentrating the REEs. The separation of REEs from each other is mainly made by chromatography.

At the beginning of REE analysis, the method of precipitation/coprecipitation was applied for the treatment of REE mixtures. The method is not applicable for the separation of trace amounts of REEs. The majority of the methods used are based on the distribution of REEs in a two-phase system, a liquid–liquid or a liquid–solid system. Various techniques have been developed for the liquid–liquid extraction (LLE), in particular the liquid phase micro-extraction. The extraction is always combined with a pre-concentration of the REEs in a single drop of extractant or in a hollow fiber filled with the extractant. Further modified techniques for special applications and for difficult REE separation have been developed. Compared to the LLE, the solid phase micro-extraction is preferred. The method is robust and easy to handle, in which the solid phase loaded with the REEs can be used directly for subsequent determination methods. At present, very new solid materials, like nanotubes, are developed and tested for solid phase extraction.

Water-assisted crystallization of mesoporous anatase TiO2 nanospheres

We report a facile water-assisted crystallization process for the conversion of amorphous sol-gel derived TiO2 into mesoporous anatase nanostructures with a high surface area and well-controlled porosity and crystallinity. As an alternative to conventional calcination methods, this approach works under very mild conditions and is therefore much desired for broad biological, environmental and catalytic applications.

Digestion of cooked meat proteins is slightly affected by age as assessed using the dynamic gastrointestinal TIM model and mass spectrometry

The main goal of the present study was to compare the degradation of meat proteins in adult and elderly digestive conditions.

Analysis of the endogenous human serum peptides by on-line extraction with restricted-access material and HPLC-MS/MS identification

The selective extraction of endogenous serum peptides has been a challenge due to the high abundant proteins present in serum. Here a simple on-line extraction of peptides from human serum using strong cation-exchange diol silica restricted-access materials (SCX-RAM) coupled with two-dimensional RP-RP liquid chromatography mass spectrometry was developed. The operation of the on-line extraction system is simple to use and does not need complex equipments. The two-dimensional RP-RP was proved to be orthogonal and efficient to separate peptides extracted from human serum.

Mass spectrometry of peptides and proteins from human blood

It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

In mesopore protein digestion: a new forthcoming strategy in proteomics

The conventional protocols for in solution or in gel protein digestion require many steps and long reaction times. The use of trypsin immobilized onto solid supports has recently captured the attention of many research groups, because these systems can speed-up protein digestion significantly. The utilization of new materials such as mesoporous silica as supports, in which enzyme and substrate are dramatically concentrated and confined in the nanospace, offers new opportunities to reduce the complexity of proteomics workflows. An overview of the procedures for in situ proteolysis of single proteins or complex protein mixtures is reported, with a special focus on porous materials used as catalysts. The challenging efforts for designing such systems aimed at mimicking the biochemistry of living cells are reviewed. Potentials, limitations and challenges of this branch of enzyme catalysis, which we indicate as in mesopore digestion, are discussed, in relation to its suitability for high-speed and high-throughput proteomics.

Nanobiocatalysis for protein digestion in proteomic analysis

The process of protein digestion is a critical step for successful protein identification in bottom-up proteomic analyses. To substitute the present practice of in-solution protein digestion, which is long, tedious, and difficult to automate, many efforts have been dedicated for the development of a rapid, recyclable and automated digestion system. Recent advances of nanobiocatalytic approaches have improved the performance of protein digestion by using various nanomaterials such as nanoporous materials, magnetic nanoparticles, and polymer nanofibers. Especially, the unprecedented success of trypsin stabilization in the form of trypsin-coated nanofibers, showing no activity decrease under repeated uses for 1 year and retaining good resistance to proteolysis, has demonstrated its great potential to be employed in the development of automated, high-throughput, and on-line digestion systems. This review discusses recent developments of nanobiocatalytic approaches for the improved performance of protein digestion in speed, detection sensitivity, recyclability, and trypsin stability. In addition, we also introduce approaches for protein digestion under unconventional energy input for protein denaturation and the development of microfluidic enzyme reactors that can benefit from recent successes of these nanobiocatalytic approaches.

The endogenous peptides of normal human serum extracted from the acetonitrile-insoluble precipitate using modified aqueous buffer with analysis by LC-ESI-Paul ion trap and Qq-TOF

Many peptides of biological or medicinal importance may be derived from proteolytic actions and are found at low concentrations in human blood fluids. Endogenous polypeptides from human serum were precipitated in acetonitrile and the precipitate was then selectively extracted with water modified by organic solvents and collected over C18 resin. Extraction of serum with C18 alone, and the acetonitrile supernatant or ultrafiltration collected over C18, served as controls. The samples were analyzed by SDS-PAGE, or C18 high pressure liquid chromatography with electrospray ionization using a Paul ion trap and Qq-TOF. Spectra were correlated without specifying an enzyme using the X!TANDEM or the Paragon algorithms. Multiple endogenous peptides from plasminogen, coagulation factors, collagens, serum amyloid, receptors, zinc finger/bromo peptide proteins, ryanodine receptor, calmodulin binding activator, erythroid differentiation factor, testes cancer antigen, extracellular matrix protein, myeloid/lymphoid leukemia 2 and many low abundance proteins were correlated by X!TANDEM with protein expect values of approximately E-16 or less. Proteins with binding sites for nucleic acids, phosphoinositides, and other cellular locations were also observed using the Qq-TOF and Paragon algorithm. Proteins with low expectation scores and overlapping peptides sequences were observed. The existence of these proteins in serum has been confirmed by tryptic digestion and LC-ESI-MS/MS. The presence of plasminogen, serum amyloid and zinc finger RNA binding proteins were confirmed by Western blot. There was agreement on the detection of endogenous peptides from low abundance proteins associated with the biology of cancer from the examination of the blood peptides by ion trap and Qq-TOF, tryptic digests of blood proteins, and Western blot.

Recent advances in mass spectrometry-based peptidome analysis

The peptidome, which is the low-molecular-weight subset of the proteome, has attracted increasing attention in recent years. However, with the interference of high-abundance protein components in complex biological mixtures (e.g., serum), selective extraction of endogenous peptides is the first and most important step before analyzing the peptidome. A number of methods and technologies have now been developed for the selective enrichment, fractionation, quantitative analysis of the endogenous peptides and their application in the potential biomarker discovery. This review will cover the methods and technologies developed in recent years for the peptidome analysis on the selective extraction, multidimensional separation and quantitative analysis, as well as their application for clinical diagnosis and biomarker discovery. The future prospects of the peptidome are also discussed.