Multi-dimensional liquid chromatography in proteomics--a review

Proteomics of Penicillium chrysogenum for a Deeper Understanding of Lead (Pb) Metal Bioremediation

Penicillium chrysogenum (P. chrysogenum), a ubiquitous filamentous fungus, has demonstrated remarkable potential in the bioremediation of lead-contaminated environments. Its inherent tolerance and bioaccumulation capacity for lead (Pb), coupled with its relatively rapid growth rate, make it an attractive candidate for bioremediation applications. This study aims to identify the proteomic changes in P. chrysogenuminduced by Pb metal stress and unravel the roles of identified proteins in molecular mechanisms and cellular responses. Untargeted proteomic analysis was carried out using a two-dimensional difference in gel electrophoresis (2D-DIGE) coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). This study reported the identification of 43 statistically significant proteins (24 upregulated and 19 downregulated, ANOVA, p ≤ 0.05; fold change ≥1.5) in P. chrysogenum as a consequence of Pb treatment. Proteins were grouped according to their function into 18 groups from which 13 proteins were related to metabolism, 11 were related to cellular process and signaling, and 19 proteins were related to information storage and processing. The current study is considered the first report about the proteomics study of P. chrysogenum under Pb stress conditions, where upregulated proteins could better explain the mechanism of tolerance and Pb toxicity removal. Our research has provided a thorough understanding of the molecular and cellular processes involved in fungal-metal interactions, paving the way for the development of innovative molecular markers for heavy metal myco-remediation. To the best of our knowledge, this study of P. chrysogenum provides valuable insights toward growing research in comprehending the metal-microbe interactions. This will facilitate development of novel molecular markers for metal bioremediation.

Ameliorating the effects of multiple stresses on agronomic traits in crops: modern biotechnological and omics approaches

While global climate change poses a significant environmental threat to agriculture, the increasing population is another big challenge to food security. To address this, developing crop varieties with increased productivity and tolerance to biotic and abiotic stresses is crucial. Breeders must identify traits to ensure higher and consistent yields under inconsistent environmental challenges, possess resilience against emerging biotic and abiotic stresses and satisfy customer demands for safer and more nutritious meals. With the advent of omics-based technologies, molecular tools are now integrated with breeding to understand the molecular genetics of genotype-based traits and develop better climate-smart crops. The rapid development of omics technologies offers an opportunity to generate novel datasets for crop species. Identifying genes and pathways responsible for significant agronomic traits has been made possible by integrating omics data with genetic and phenotypic information. This paper discusses the importance and use of omics-based strategies, including genomics, transcriptomics, proteomics and phenomics, for agricultural and horticultural crop improvement, which aligns with developing better adaptability in these crop species to the changing climate conditions.

The atrial and ventricular myocardial proteome of end-stage lamin heart disease

Lamins A/C (encoded by LMNA gene) can lead to dilated cardiomyopathy (DCM). This pilot study sought to explore the postgenomic phenotype of end-stage lamin heart disease. Consecutive patients with end-stage lamin heart disease (LMNA-group, n = 7) and ischaemic DCM (ICM-group, n = 7) undergoing heart transplantation were prospectively enrolled. Samples were obtained from left atrium (LA), left ventricle (LV), right atrium (RA), right ventricle (RV) and interventricular septum (IVS), avoiding the infarcted myocardial segments in the ICM-group. Samples were analysed using a discovery 'shotgun' proteomics approach. We found that 990 proteins were differentially abundant between LMNA and ICM samples with the LA being most perturbed (16-fold more than the LV). Abundance of lamin A/C protein was reduced, but lamin B increased in LMNA LA/RA tissue compared to ICM, but not in LV/RV. Carbonic anhydrase 3 (CA3) was over-abundant across all LMNA tissue samples (LA, LV, RA, RV, and IVS) when compared to ICM. Transthyretin was more abundant in the LV/RV of LMNA compared to ICM, while sarcomeric proteins such as titin and cardiac alpha-cardiac myosin heavy chain were generally less abundant in RA/LA of LMNA. Protein expression profiling and enrichment analysis pointed towards sarcopenia, extracellular matrix remodeling, deficient myocardial energetics, redox imbalances, and abnormal calcium handling in LMNA samples. Compared to ICM, end-stage lamin heart disease is a biventricular but especially a biatrial disease appearing to have an abundance of lamin B, CA3 and transthyretin, potentially hinting to compensatory responses.

The Research Progress of Bioactive Peptides Derived from Traditional Natural Products in China

Traditional natural products in China have a long history and a vast pharmacological repertoire that has garnered significant attention due to their safety and efficacy in disease prevention and treatment. Among the bioactive components of traditional natural products in China, bioactive peptides (BPs) are specific protein fragments that have beneficial effects on human health. Despite many of the traditional natural products in China ingredients being rich in protein, BPs have not received sufficient attention as a critical factor influencing overall therapeutic efficacy. Therefore, the purpose of this review is to provide a comprehensive summary of the current methodologies for the preparation, isolation, and identification of BPs from traditional natural products in China and to classify the functions of discovered BPs. Insights from this review are expected to facilitate the development of targeted drugs and functional foods derived from traditional natural products in China in the future.

Effect of NaCl stress on exoproteome profiles of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H

Salt stress can affect survival, multiplication and ability of plant growth promoting microorganisms to enhance plant growth. Changes in a microbe's proteome profile is one of the mechanisms employed by PGPM to enhance tolerance of salt stress. This study was focused on understanding changes in the exoproteome profile of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H when exposed to salt stress. The strains were cultured in 100 mL M13 (B. amyloliquefaciens) and 100 mL De man, Rogosa and Sharpe (MRS) (L. helveticus) media, supplemented with 200 and 0 mM NaCl (control), at pH 7.0. The strains were then incubated for 48 h (late exponential growth phase), at 120 rpm and 30 (B. amyloliquefaciens) and 37 (L. helveticus) °C. The microbial cultures were then centrifuged and filtered sterilized, to obtain cell free supernatants whose proteome profiles were studied using LC-MS/MS analysis and quantified using scaffold. Results of the study revealed that treatment with 200 mM NaCl negatively affected the quantity of identified proteins in comparison to the control, for both strains. There was upregulation and downregulation of some proteins, even up to 100%, which resulted in identification of proteins significantly unique between the control or 200 mM NaCl (p ≤ 0.05), for both microbial species. Proteins unique to 200 mM NaCl were mostly those involved in cell wall metabolism, substrate transport, oxidative stress tolerance, gene expression and DNA replication and repair. Some of the identified unique proteins have also been reported to enhance plant growth. In conclusion, based on the results of the work described here, PGPM alter their exoproteome profile when exposed to salt stress, potentially upregulating proteins that enhance their tolerance to this stress.

Proteomics-Driven Biomarkers in Pancreatic Cancer

Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.

Combining offline high performance liquid chromatography fractionation of peptides and intact proteins to enhance proteome coverage in bottom-up proteomics

Offline peptide separation (PS) using high-performance liquid chromatography (HPLC) is currently used to enhance liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection of proteins. In search of more effective methods for enhancing MS proteome coverage, we developed a robust method for intact protein separation (IPS), an alternative first-dimension separation technique, and explored additional benefits that it offers. Comparing IPS to the traditional PS method, we found that both enhance detection of unique protein IDs to a similar magnitude, though in diverse ways. IPS was especially effective in serum, which has a small number of extremely high abundance proteins. PS was more effective in tissues with fewer dominating high-abundance proteins and was more effective in enhancing detection of post-translational modifications (PTMs). Combining the IPS and PS methods together (IPS+PS) was especially beneficial, enhancing proteome detection more than either method could independently. The comparison of IPS+PS versus six PS fractionation pools increased total number of proteins IDs by nearly double, while also significantly increasing number of unique peptides detected per protein, percent peptide sequence coverage of each protein, and detection of PTMs. This IPS+PS combined method requires fewer LC-MS/MS runs than current PS methods would need to obtain similar improvements in proteome detection, and it is robust, time- and cost-effective, and generally applicable to various tissue and sample types.

Thin layer chromatography/desorption flame-induced atmospheric pressure chemical ionization/mass spectrometry for the analysis of volatile and semi-volatile mixtures

Flame-induced atmospheric pressure chemical ionization (FAPCI) has been used to directly characterize chemical compounds on a glass rod and drug tablet surfaces. In this study, FAPCI was further applied to interface thin layer chromatography (TLC) and mass spectrometry (MS) for mixture analysis.

METHODS

A micro-sized oxyacetylene flame was generated using a small concentric tube system. Hot gas flow and primary reactive species from the micro-flame were directed toward a developed TLC gel plate to thermally desorb and ionize analytes on the gel surface. The resulting analyte ions subsequently entered the MS inlet for detection.

RESULTS

A 1-1.5-mm-wide light-brown line was observed on the TLC plate after the desorption FAPCI/MS (DFAPCI/MS) analysis, revealing that the gel surface withstood a high temperature from the impact of the micro-flame. Volatile and semi-volatile chemical compounds, including amine and amide standards, drugs, and aromatherapy oils, were successfully desorbed, ionized, and detected using this TLC/DFAPCI/MS. The limit of detection of TLC-DFAPCI/MS was determined to be 5 ng/spot for dibenzylamine and ethenzamide.

CONCLUSIONS

TLC/DFAPCI/MS is one of the simplest TLC-MS interfaces showing the advantages such as low costs and an easy set up. The technique is useful for characterizing thermally stable volatile and semi-volatile compounds in a mixture.

Liquid chromatography and capillary electrophoresis in glycomic and glycoproteomic analysis

Glycosylation is one of the most significant and abundant post-translational modifications in cells. Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycomic and glycoproteomic analysis is highly challenging because of the large diversity of structures, low abundance, site-specific heterogeneity, and poor ionization efficiency of glycans and glycopeptides in mass spectrometry (MS). MS is a key tool for characterization of glycans and glycopeptides. However, MS alone does not always provide full structural and quantitative information for many reasons, and thus MS is combined with some separation technique. This review focuses on the role of separation techniques used in glycomic and glycoproteomic analyses, liquid chromatography and capillary electrophoresis. The most important separation conditions and results are presented and discussed.

Graphical abstract

Insight Into the Molecular Mechanisms Underpinning the Mycoremediation of Multiple Metals by Proteomic Technique

We investigated the fungus Aspergillus fumigatus PD-18 responses when subjected to the multimetal combination (Total Cr, Cd2+, Cu2+, Ni2+, Pb2+, and Zn2+) in synthetic composite media. To understand how multimetal stress impacts fungal cells at the molecular level, the cellular response of A. fumigatus PD-18 to 30 mg/L multimetal stress (5 mg/L of each heavy metal) was determined by proteomics. The comparative fungal proteomics displayed the remarkable inherent intracellular and extracellular mechanism of metal resistance and tolerance potential of A. fumigatus PD-18. This study reported 2,238 proteins of which 434 proteins were exclusively expressed in multimetal extracts. The most predominant functional class expressed was for cellular processing and signaling. The type of proteins and the number of proteins that were upregulated due to various stress tolerance mechanisms were post-translational modification, protein turnover, and chaperones (42); translation, ribosomal structure, and biogenesis (60); and intracellular trafficking, secretion, and vesicular transport (18). In addition, free radical scavenging antioxidant proteins, such as superoxide dismutase, were upregulated upto 3.45-fold and transporter systems, such as protein transport (SEC31), upto 3.31-fold to combat the oxidative stress caused by the multiple metals. Also, protein–protein interaction network analysis revealed that cytochrome c oxidase and 60S ribosomal protein played key roles to detoxify the multimetal. To the best of our knowledge, this study of A. fumigatus PD-18 provides valuable insights toward the growing research in comprehending the metal microbe interactions in the presence of multimetal. This will facilitate in development of novel molecular markers for contaminant bioremediation.

Recent Advances in Solid-Phase Extraction as a Platform for Sample Preparation in Biomarker Assay

Low levels of biomarkers and the complexity of bio sample make the analytical assay of several biomarkers a challenging issue. Suitable sample preparation run remain a vital part of the puzzle of diagnostic level. Enhancing the detection limit of bioanalytical methods start during the sample preparation procedure. A robust sample preparation method is needed to evaluate the number of biomarkers. As worldwide environmental issues attract expanding consideration, all the more harmless to the ecosystem investigations are liked. Solid-phase extraction (SPE) is an appealing strategy among the sample treatment methods due to the versatility of sorbent materials, less solvent consumption, and compatibility with analytical devices. Miniaturization of the SPE gives the chance to integrate the other analytical steps in a single run, known as an easy-to-use and effective method. SPE utilizes various SPE sorbent beds such as packed beads, porous polymer monoliths, molecularly imprinted polymers, membranes, or other magnetic form microstructures to achieve high surface-to-volume ratio and appropriate chemical properties effective extraction. Also, SPE is the methodology of interest to fulfill high recovery and efficiency demands. In this review, we intend to explain more recent methods for the rational design of SPE and miniaturized SPE to determine biomarkers from biological media. The headlines are subdivided into (1) packing materials in SPE, (2) setups for sample preparation by magnetic SPE, and (3) and future perspective for the application of SPE in sample preparation for analysis of biomarkers.

Nano liquid chromatography, an updated review

Low flow chromatography has a rich history of innovation but has yet to reach widespread implementation in bioanalytical applications. Improvements in pump technology, microfluidic connections, and nano-electrospray sources for mass spectrometry have laid the groundwork for broader application, and innovation in this space has accelerated in recent years. This article reviews the instrumentation used for nano-flow liquid chromatography , the types of columns employed, and strategies for multi-dimensionality of separations, which is key to the future state of the technique to the high-throughput needs of modern bioanalysis. An update of the current applications where nano-LC is widely used, such as proteomics and metabolomics, is discussed. But the trend towards biopharmaceutical development of increasingly complex, targeted, and potent therapeutics for the safe treatment of disease drives the need for ultimate selectivity and sensitivity of our analytical platforms for targeted quantitation in a regulated space. The selectivity needs are best addressed by mass spectrometric detection, especially at high resolutions, and exquisite sensitivity is provided by nano-electrospray ionization as the technology continues to evolve into an accessible, robust, and easy to use platform.

Proteomic Analysis of Plasma Markers in Patients Maintained on Antipsychotics: Comparison to Patients Off Antipsychotics and Normal Controls

BACKGROUND

Schizophrenia (SZ) and bipolar disorder (BD) share many features: overlap in mood and psychotic symptoms, common genetic predisposition, treatment with antipsychotics (APs), and similar metabolic comorbidities. The pathophysiology of both is still not well defined, and no biomarkers can be used clinically for diagnosis and management. This study aimed to assess the plasma proteomics profile of patients with SZ and BD maintained on APs compared to those who had been off APs for 6 months and to healthy controls (HCs).

METHODS

We analyzed the data using functional enrichment, random forest modeling to identify potential biomarkers, and multivariate regression for the associations with metabolic abnormalities.

RESULTS

We identified several proteins known to play roles in the differentiation of the nervous system like NTRK2, CNTN1, ROBO2, and PLXNC1, which were downregulated in AP-free SZ and BD patients but were "normalized" in those on APs. Other proteins (like NCAM1 and TNFRSF17) were "normal" in AP-free patients but downregulated in patients on APs, suggesting that these changes are related to medication's effects. We found significant enrichment of proteins involved in neuronal plasticity, mainly in SZ patients on APs. Most of the proteins associated with metabolic abnormalities were more related to APs use than having SZ or BD. The biomarkers identification showed specific and sensitive results for schizophrenia, where two proteins (PRL and MRC2) produced adequate results.

CONCLUSIONS

Our results confirmed the utility of blood samples to identify protein signatures and mechanisms involved in the pathophysiology and treatment of SZ and BD.

Peptidomics and proteogenomics: background, challenges and future needs

INTRODUCTION

With available genomic data and related information, it is becoming possible to better highlight mutations or genomic alterations associated with a particular disease or disorder. The advent of high-throughput sequencing technologies has greatly advanced diagnostics, prognostics, and drug development.

AREAS COVERED

Peptidomics and proteogenomics are the two post-genomic technologies that enable the simultaneous study of peptides and proteins/transcripts/genes. Both technologies add a remarkably large amount of data to the pool of information on various peptides associated with gene mutations or genome remodeling. Literature search was performed in the PubMed database and is up to date.

EXPERT OPINION

This article lists various techniques used for peptidomic and proteogenomic analyses. It also explains various bioinformatics workflows developed to understand differentially expressed peptides/proteins and their role in disease pathogenesis. Their role in deciphering disease pathways, cancer research, and biomarker discovery using biofluids is highlighted. Finally, the challenges and future requirements to overcome the current limitations for their effective clinical use are also discussed.

Downstream Processing of Therapeutic Peptides by Means of Preparative Liquid Chromatography

The market of biomolecules with therapeutic scopes, including peptides, is continuously expanding. The interest towards this class of pharmaceuticals is stimulated by the broad range of bioactivities that peptides can trigger in the human body. The main production methods to obtain peptides are enzymatic hydrolysis, microbial fermentation, recombinant approach and, especially, chemical synthesis. None of these methods, however, produce exclusively the target product. Other species represent impurities that, for safety and pharmaceutical quality reasons, must be removed. The remarkable production volumes of peptide mixtures have generated a strong interest towards the purification procedures, particularly due to their relevant impact on the manufacturing costs. The purification method of choice is mainly preparative liquid chromatography, because of its flexibility, which allows one to choose case-by-case the experimental conditions that most suitably fit that particular purification problem. Different modes of chromatography that can cover almost every separation case are reviewed in this article. Additionally, an outlook to a very recent continuous chromatographic process (namely Multicolumn Countercurrent Solvent Gradient Purification, MCSGP) and future perspectives regarding purification strategies will be considered at the end of this review.

Proteomics of Cellular Response to Stress: Taking Control of False Positive Results

One of the main goals of quantitative proteomics is molecular profiling of cellular response to stress at the protein level. To perform this profiling, statistical analysis of experimental data involves multiple testing of a hypothesis about the equality of protein concentrations between the cells under normal and stress conditions. This analysis is then associated with the multiple testing problem dealing with the increased chance of obtaining false positive results. A number of solutions to this problem are known, yet, they may lead to the loss of potentially important biological information when applied with commonly accepted thresholds of statistical significance. Using the proteomic data obtained earlier for the yeast samples containing proteins at known concentrations and the biological models of early and late cellular responses to stress, we analyzed dependences of distributions of false positive and false negative rates on the protein fold changes and thresholds of statistical significance. Based on the analysis of the density of data points in the volcano plots, Benjamini-Hochberg method, and gene ontology analysis, visual approach for optimization of the statistical threshold and selection of the differentially regulated proteins has been suggested, which could be useful for researchers working in the field of quantitative proteomics.

Static vs. Dynamic Electrostatic Repulsion Reversed Phase Liquid Chromatography: Solutions for Pharmaceutical and Biopharmaceutical Basic Compounds

Many efforts have been made to separate basic compounds, which are challenging to resolve in reversed phase liquid chromatography. In this process, they are strongly retained and the peak shape undergoes significant distortion. The principal origin of this has been identified with the non-negligible interaction with residual deprotonated silanols. Consequently, all solutions that efficiently shield silanols are being sought. This review is an upgrade on the use of the electrostatic repulsion reversed phase (ERRP) approach: retention of bases, in protonated form, can be achieved by modulating the charge repulsion caused by the presence of positive charges in the chromatographic system. This study successfully (i) introduced fixed positive charges in the structure of stationary phases, (ii) used cationic and hydrophobic additives in the mobile phase, and (iii) used the ERRP-like approach employed at the preparative level for peptide purification.

Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics

Field asymmetric ion mobility spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity and enables more proteins to be identified by providing additional gas-phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications, an 8% increase in proteoform identifications, and an improvement in proteoform identification compared to samples analyzed without FAIMS. In addition, utilization of FAIMS resulted in the identification of proteins encoded by lower-abundance mRNA transcripts. These improvements were attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications.

Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support

RATIONALE

One of the important steps in initial data processing of peptide mass spectra is the detection of peptide features in full-range mass spectra. Ion mobility offers advantages over previous methods performing this detection by providing an additional structure-specific separation dimension. However, there is a lack of open-source software that utilizes these advantages and detects peptide features in mass spectra acquired along with ion mobility data using new instruments such as timsTOF and/or FAIMS-Orbitrap.

METHODS

Recently, a utility called Dinosaur was presented, which provides an efficient way for feature detection in peptide ion mass spectra. In this work we extended its functionality by developing Biosaur software to fully employ the additional information provided by ion mobility data. Biosaur was developed using the Python 3.8 programming language.

RESULTS

Biosaur supports the processing of data acquired using mass spectrometers with ion mobility capabilities, specifically timsTOF and FAIMS. In addition, it processes mass spectra obtained in negative ion mode and reports cosine correlation table for peptide features which is useful for differentiation between in-source fragments and semi-tryptic peptides.

CONCLUSIONS

Biosaur is a utility for detecting peptide features in liquid chromatography-mass spectra with ion mobility and negative ion supports. The software is distributed with an open-source APACHE 2.0 license and is freely available on Github: https://github.com/abdrakhimov1/Biosaur.

Robustness and Ruggedness of Isoelectric Focusing and Superficially Porous Liquid Chromatography with Fourier Transform Mass Spectrometry

An investigation of a multidimensional proteomics workflow composed of off-gel isoelectric focusing (IEF) and superficially porous liquid chromatography (SPLC) with Fourier transform mass spectrometry (FTMS) was completed in order to assess various figures of merit associated with intact protein measurements. Triplicate analysis performed at both high and low FTMS resolutions on the E. coli proteome resulted in ∼900 redundant proteoforms from 3 to 95 kDa. Normalization of the chromatographic axis to identified proteoforms enabled reproducible physicochemical property measurements between proteome replicates with inter-replicate variances of ±3 ppm mass error for proteoforms <30 kDa, ±1.1 Da for proteins >30 kDa, ±12 s retention time error, and ±0.21 pI units. The results for E. coli and standard proteins revealed a correlation between pI precision and proteoform abundance with species detected in multiple IEF fractions exhibiting pI precisions less than the theoretical resolution of the off-gel system (±0.05 vs ±0.17, respectively). Evaluation of differentially modified proteoforms of standard proteins revealed that high sample loads (100s μgrams) change the IEF pH gradient profile, leading to sample broadening that facilitates resolution of charged post-translational modifications (e.g., phosphorylation, sialylation). Despite the impact of sample load on IEF resolution, results on standard proteins measured directly or after being spiked into E. coli demonstrated that the reproducibility of the workflow permitted recombination of the MS signal across IEF fractions in a manner supporting the evaluation of three label-free quantitation metrics for intact protein studies (proteoforms, proteoform ratios, and protein) over 102-103 sample amount with low femtomole detection limits.

Molecular dynamics simulations of amino acid adsorption and transport at the acetonitrile–water–silica interface: the role of side chains

The solvation and transport of amino acid residues at liquid–solid interfaces have great importance for understanding the mechanism of separation of biomolecules in liquid chromatography. This study uses umbrella sampling molecular dynamics simulations to study the adsorption and transport of three amino acid molecules with different side chains (phenylalanine (Phe), leucine (Leu) and glutamine (Gln)) at the silica–water–acetonitrile interface in liquid chromatography. Free energy analysis shows that the Gln molecule has stronger binding affinity than the other two molecules, indicating the side chain polarity may play a primary role in adsorption at the liquid–solid interface. The Phe molecule with a phenyl side chain exhibits stronger adsorption free energy than Leu with a non-polar side chain, which can be ascribed to the better solvated configuration of Phe. Further analysis of molecular orientations found that the amino acid molecules with apolar side chains (Phe and Leu) have ‘standing up’ configurations at their stable adsorption state, where the polar functional groups are close to the interface and the side chain is far from the interface, whereas the amino acid molecule with a polar side chain (Gln) chooses the ‘lying’ configuration, and undergoes a sharp orientation transition when the molecule moves away from the silica surface. Extending our simulation studies to systems with different solute concentrations reveals that there is a decrease in the adsorption free energy as well as surface diffusion as the solute concentration increases, which is related to the crowding in the interfacial layers. This simulation study gives a detailed microscopic description of amino acid molecule solvation and transport at the acetonitrile–water–silica interface in liquid chromatography and will be helpful for understanding the retention mechanism for amino acid separation.

The solvation and transport of amino acid residues at liquid–solid interfaces have great importance for understanding the mechanism of separation of biomolecules in liquid chromatography.

Proteomic Analysis of Chr 18 Proteins Using 2D Fractionation

One of the main goals of the Chromosome-Centric Human Proteome Project (C-HPP) is detection of "missing proteins" (PE2-PE4). Using the UPS2 (Universal proteomics standard 2) set as a model to simulate the range of protein concentrations in the cell, we have previously shown that 2D fractionation enables the detection of more than 95% of UPS2 proteins in a complex biological mixture. In this study, we propose a novel experimental workflow for protein detection during the analysis of biological samples. This approach is extremely important in the context of the C-HPP and the neXt-MP50 Challenge, which can be solved by increasing the sensitivity and the coverage of the proteome encoded by a particular human chromosome. In this study, we used 2D fractionation for in-depth analysis of the proteins encoded by human chromosome 18 (Chr 18) in the HepG2 cell line. Use of 2D fractionation increased the sensitivity of the SRM SIS method by 1.3-fold (68 and 88 proteins were identified by 1D fractionation and 2D fractionation, respectively) and the shotgun MS/MS method by 2.5-fold (21 and 53 proteins encoded by Chr 18 were detected by 1D fractionation and 2D fractionation, respectively). The results of all experiments indicate that 111 proteins encoded by human Chr 18 have been identified; this list includes 42% of the Chr 18 protein-coding genes and 67% of the Chr 18 transcriptome species (Illumina RNaseq) in the HepG2 cell line obtained using a single sample. Corresponding mRNAs were not registered for 13 of the detected proteins. The combination of 2D fractionation technology with SRM SIS and shotgun mass spectrometric analysis did not achieve full coverage, i.e., identification of at least one protein product for each of the 265 protein-coding genes of the selected chromosome. To further increase the sensitivity of the method, we plan to use 5-10 crude synthetic peptides for each protein to identify the proteins and select one of the peptides based on the obtained mass spectra for the synthesis of an isotopically labeled standard for subsequent quantitative analysis. Data are available via ProteomeXchange with the identifier PXD019263.

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics

Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution. Multidimensional separations provide enhanced peak capacity and reduce sample complexity, which enables mass spectrometry to analyze more proteins with high sensitivity. Although two-dimensional (2D) separations have been widely used since the early period of proteomics, three-dimensional (3D) separation was barely used by low reproducibility of separation, increased analysis time in mass spectrometry. With developments of novel microscale techniques such as nano-UPLC and improvements of mass spectrometry, the 3D separation becomes a reliable and practical selection. This review summarizes existing offline and online 3D-LC platforms developed for proteomics and their applications. In detail, setups and implementation of those systems as well as their advances are outlined. The performance of those platforms is also discussed and compared with the state-of-the-art 2D-LC. In addition, we provide some perspectives on the future developments and applications of 3D-LC in proteomics.

Mass spectrometry-based protein identification in proteomics-a review

Statistically, accurate protein identification is a fundamental cornerstone of proteomics and underpins the understanding and application of this technology across all elements of medicine and biology. Proteomics, as a branch of biochemistry, has in recent years played a pivotal role in extending and developing the science of accurately identifying the biology and interactions of groups of proteins or proteomes. Proteomics has primarily used mass spectrometry (MS)-based techniques for identifying proteins, although other techniques including affinity-based identifications still play significant roles. Here, we outline the basics of MS to understand how data are generated and parameters used to inform computational tools used in protein identification. We then outline a comprehensive analysis of the bioinformatics and computational methodologies used in protein identification in proteomics including discussing the most current communally acceptable metrics to validate any identification.

Development of Injectable Amniotic Membrane Matrix for Postmyocardial Infarction Tissue Repair

Ischemic heart disease represents the leading cause of death worldwide. Heart failure following myocardial infarction (MI) is associated with severe fibrosis formation and cardiac remodeling. Recently, injectable hydrogels have emerged as a promising approach to repair the infarcted heart and improve heart function through minimally invasive administration. Here, a novel injectable human amniotic membrane (hAM) matrix is developed to enhance cardiac regeneration following MI. Human amniotic membrane is isolated from human placenta and engineered to be a thermoresponsive, injectable gel around body temperature. Ultrasound-guided injection of hAM matrix into rat MI hearts significantly improves cardiac contractility, as measured by ejection fraction (EF), and decrease fibrosis. The results of this study demonstrate the feasibility of engineering as an injectable hAM matrix and its efficacy in attenuating degenerative changes in cardiac function following MI, which may have broad applications in tissue regeneration.

Online Comprehensive High pH Reversed Phase × Low pH Reversed Phase Approach for Two-Dimensional Separations of Intact Proteins in Top-Down Proteomics

A proof-of-concept study is presented on the use of comprehensive two-dimensional liquid chromatography mass spectrometry (LC × LC-MS) for the separation of intact protein mixtures using a different mobile phase pH in each dimension. This system utilizes mass spectrometry (MS) friendly pH modifiers for the online coupling of high pH reversed phase liquid chromatography (HPH-RPLC) in the first dimension (¹D) followed by low pH reversed phase liquid chromatography (LPH-RPLC) in the second dimension (²D). Owing to the ionic nature of proteins, the use of a different mobile phase pH was successful to provide altered selectivity between the two dimensions, even for closely related protein variants, such as bovine cytochrome c and equine cytochrome c, which differ by only three amino acids. Subminute gradient separation of proteins in the second dimension was successful to minimize analysis time, while maintaining high peak capacity. Unlike peptides, the elution order of studied proteins did not follow their isoelectric points, where acidic proteins would be expected to be more retained at low pH (and basic proteins at high pH). The steep elution isotherms (on-off retention mechanism) of proteins and the very steep gradients utilized in the second-dimension column succeeded in overcoming pH and organic solvent content mismatch. The utility of the system was demonstrated with a mixture of protein standards and an Escherichia coli protein mixture.

Differentially Expressed Protein Are Involved in Dynamic Changes of Catechins Contents in Postharvest Tea Leaves under Different Temperatures

In this study, isobaric tags for relative and absolute quantitation (iTRAQ) technology were used to investigate three samples from postharvest tea leaves that were treated at room temperature (25 °C, control group), high temperature (38 °C), and low temperature (4 °C) for 4 h. In heat and cold treatments, a total of 635 and 566 differentially expressed proteins (DEPs) were determined, respectively. DEPs were annotated to GO and KEGG databases, which revealed that DEPs involved in various aspects of biological process. Three catechins-related DEPs, CsCHI, CsF3H, and CsANR, were identified. Both catechins contents and the expression profiles of catechins biosynthesis-related genes changed significantly under different temperature treatments. The correlations between catechins contents, gene expression profiles, and DEPs were analyzed. This study provides potential new insights into the molecular basis for tea production of postharvest leaves and catechins content changes at diverse temperature conditions and will guide the improvement of tea-processing technology.

Comparative Analysis of Blood Plasma Proteome in Patients with Renal Cell Carcinoma

Comparative mass spectrometric analysis of protein composition was carried out in 36 blood plasma specimens from patients with renal cell carcinoma and 20 specimens from donors. Analysis of protein composition of plasma specimens devoid of the major protein fractions showed a 20-50% higher level of protein identifications in patient' specimens. Specimens of the control and experimental series were similar by protein composition, 70-80% identifications in experimental and control series coinciding. High similarity of biological processes with participation of the proteins identified in both series was observed. The greater part of proteins in both series were located extracellularly and were exosomal (specimens from renal cancer patients) or vesicular (specimens from healthy volunteers).

Experimental and numerical study of band-broadening effects associated with analyte transfer in microfluidic devices for spatial two-dimensional liquid chromatography created by additive manufacturing

Conventional one-dimensional column-based liquid chromatographic (LC) systems do not offer sufficient separation power for the analysis of complex mixtures. Column-based comprehensive two-dimensional liquid chromatography offers a higher separation power, yet suffers from instrumental complexity and long analysis times. Spatial two-dimensional liquid chromatography can be considered as an alternative to column-based approaches. The peak capacity of the system is ideally the product of the peak capacities of the two dimensions, yet the analysis time remains relatively short due to parallel second-dimension separations. Aspects affecting the separation efficiency of this type of systems include flow distribution to homogeneously distribute the mobile phase for the second-dimension (²D) separation, flow confinement during the first-dimension (¹D) separation, and band-broadening effects during analyte transfer from the ¹D separation channel to the ²D separation area. In this study, the synergy between computational fluid dynamics (CFD) simulations and rapid prototyping was exploited to address band broadening during the ²D development and analyte transfer from ¹D to ²D. Microfluidic devices for spatial two-dimensional liquid chromatography were designed, simulated, 3D-printed and tested. The effects of presence and thickness of spacers in the ²D separation area were addressed and leaving these out proved to be the most efficient solution regarding band broadening reduction. The presence of a stationary-phase material in the ¹D channel had a great effect on the analyte transfer from the ¹D to the ²D and the resulting band broadening. Finally, pressure limit of the fabricated devices and printability are discussed.

Investigating the Role of Mitochondria in Type 2 Diabetes - Lessons from Lipidomics and Proteomics Studies of Skeletal Muscle and Liver

Mitochondrial dysfunction is discussed as a key player in the pathogenesis of type 2 diabetes mellitus (T2Dm), a highly prevalent disease rapidly developing as one of the greatest global health challenges of this century. Data however about the involvement of mitochondria, central hubs in bioenergetic processes, in the disease development are still controversial. Lipid and protein homeostasis are under intense discussion to be crucial for proper mitochondrial function. Consequently proteomics and lipidomics analyses might help to understand how molecular changes in mitochondria translate to alterations in energy transduction as observed in the healthy and metabolic diseases such as T2Dm and other related disorders. Mitochondrial lipids integrated in a tool covering proteomic and functional analyses were up to now rarely investigated, although mitochondrial lipids might provide a possible lynchpin in the understanding of type 2 diabetes development and thereby prevention. In this chapter state-of-the-art analytical strategies, pre-analytical aspects, potential pitfalls as well as current proteomics and lipidomics-based knowledge about the pathophysiological role of mitochondria in the pathogenesis of type 2 diabetes will be discussed.

Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry

Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.

Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation

Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.

A novel two-dimensional liquid chromatography - Mass spectrometry method for direct drug impurity identification from HPLC eluent containing ion-pairing reagent in mobile phases

In this study, a novel two dimensional liquid chromatography - mass spectrometry (2D-LC-MS) method with use of a weak anion exchange column between the 1st DLC RP column and the 2nd DLC RP column (RP1-WAX-RP2) was developed and applied to identify drug impurities from MS incompatible mobile phases containing sodium 1-octanesulfonate and non-volatile buffer. The 1st DLC conditions follow exactly the original standard HPLC method recorded in Chinese Pharmacopeia (ChP), European Pharmacopeia (EP) or US Pharmacopeia (USP). An impurity fraction was collected with a built-in sample loop (100 μL) and transferred to the WAX column where 1-octanesulfonate and phosphate were trapped and removed. While, the impurity and other cations were eluted to the 2nd D column (RP2) for separation and identification by connected IT-TOF MS. Methods were programmed and applied to identify impurities in two generic drugs, sulpiride (hydrophilic drug with logP 0.57) and dobutamine (hydrophobic drug with logP 3.6). The results indicate that the methods based on RP1-WAX-RP2 column configuration offer a feasible solution for direct impurity identification in generic drug product or API without needs of off-line desalting from the MS incompatible mobile phases containing ion-pairing reagent and non-volatile buffer.

The use of chemical probes to detect the proteomics of renal tubular injury induced by maleic acid

Maleic acid (MA), an industrial raw material, was found to be illegally added to edible starch-based food products in Taiwan in 2013, a practice unheard of in most of the world. MA has been associated with renal dysfunction in many experimental animal studies. In this study, we developed chemical probes to investigate protein-protein interactions between MA and renal proteins. In the fabrication of the MA probes, we used silicon dioxide (SiO₂) modified with a silanized linker (3-aminopropyl triethoxyslane, APTES) to generate MA with APTES-SiO₂ particles. The probes were then incubated with the cell lysates of normal human kidney cell lines (HK-2) and subjected to MS/MS for identifying several MA-related proteins, including nucleophosmin, neutral alpha-glucosidase AB, translocon-associated protein subunit alpha, elongation factor 1-gamma, 60S acidic ribosomal protein P0-like, and heat shock protein (HSP 90-alpha and beta). Based on our findings, we believed that the probe can potentially be used to identify and detect the target proteins and help characterize a network of MA protein-protein interactions.

Enhanced Peptide Detection Toward Single-Neuron Proteomics by Reversed-Phase Fractionation Capillary Electrophoresis Mass Spectrometry

The ability to detect peptides and proteins in single cells is vital for understanding cell heterogeneity in the nervous system. Capillary electrophoresis (CE) nanoelectrospray ionization (nanoESI) provides high-resolution mass spectrometry (HRMS) with trace-level sensitivity, but compressed separation during CE challenges protein identification by tandem HRMS with limited MS/MS duty cycle. Here, we supplemented ultrasensitive CE-nanoESI-HRMS with reversed-phase (RP) fractionation to enhance identifications from protein digest amounts that approximate to a few mammalian neurons. An ~1 to 20 μg neuronal protein digest was fractionated on a RP column (ZipTip), and 1 ng to 500 pg of peptides were analyzed by a custom-built CE-HRMS system. Compared with the control (no fractionation), RP fractionation improved CE separation (theoretical plates ~274,000 versus 412,000 maximum, resp.), which enhanced detection sensitivity (2.5-fold higher signal-to-noise ratio), minimized co-isolation spectral interferences during MS/MS, and increased the temporal rate of peptide identification by up to ~57%. From 1 ng of protein digest (<5 neurons), CE with RP fractionation identified 737 protein groups (1,753 peptides), or ~480 protein groups (~1,650 peptides) on average per analysis. The approach was scalable to 500 pg of protein digest (~a single neuron), identifying 225 protein groups (623 peptides) in technical triplicates, or 141 protein groups on average per analysis. Among identified proteins, 101 proteins were products of genes that are known to be transcriptionally active in single neurons during early development of the brain, including those involved in synaptic transmission and plasticity and cytoskeletal organization. Graphical abstract ᅟ.

Using proteomics as a powerful tool to develop a vaccine against Mediterranean visceral leishmaniasis

Visceral leishmaniasis (VL) is a tropical infectious disease, which is called Mediterranean visceral leishmaniasis (MVL) in the Mediterranean area. In spite of many attempts, no effective commercial vaccine exists for MVL. To find new targets for developing antileishmanial vaccines, knowing parasite antigens that provoke the immune system are on demand. Nowadays, proteomics methods are defined as approaches for analysis of protein profiling of different cells. Within this framework, detection of new antigens is becoming more facilitated. In this review, we aimed to introduce possible targets using proteomics so; they could be used as candidates for developing vaccines against MVL. It can shed new light in the near future on the development of promising vaccines for MVL.

A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics

The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.

Current state of bioanalytical chromatography in clinical analysis

Chromatographic methods have become popular in clinical analysis in both routine and research laboratories.