Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals

Methods to Investigate the Secretome of Senescent Cells

The word "secretome" was first used to describe the proteins that cells secrete under different circumstances; however, recent studies have proven the existence of other molecules such as RNA and chemical compounds in the secretome. The study of secretome has significance for the diagnosis and treatment of disease as it provides insight into cellular functions, including immune responses, development, and homeostasis. By halting cell division, cellular senescence plays a role in both cancer defense and aging by secreting substances known as senescence-associated secretory phenotypes (SASP). A variety of techniques could be used to analyze the secretome: protein-based approaches like mass spectrometry and protein microarrays, nucleic acid-based methods like RNA sequencing, microarrays, and in silico prediction. Each method offers unique advantages and limitations in characterizing secreted molecules. Top-down and bottom-up strategies for thorough secretome analysis are became possible by mass spectrometry. Understanding cellular function, disease causes, and proper treatment targets is aided by these methodologies. Their approaches, benefits, and drawbacks will all be discussed in this review.

Two-Dimensional Gel Electrophoresis in Studies of Flower and Leaf Proteome of Common Buckwheat

Two-dimensional gel electrophoresis (2-DE) is a proteomic tool used for the separation of protein mixtures according to protein isoelectric point and molecular mass. Although gel-free quantitative and qualitative proteomic study techniques are now available, 2-DE remains a useful analytical tool. The presented protocol was performed to analyze the flower and leaf proteome of common buckwheat using 24 cm immobilized pH gradient strips (pH 4-7) and visualization of proteins on gels via colloidal Coomassie G-250 staining.

Carotenoids in Health as Studied by Omics-Related Endpoints

Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor κB and nuclear factor erythroid 2-related factor 2. Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor and peroxisome proliferator-activated receptors, which play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes and proteins implicated in oxidative stress and inflammation, antioxidation, and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)omics-related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, as well as metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells, or other tissue cellular extracts. In this review, we highlight the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.

Hydrophobicity and molecular mass-based separation method for autoantibody discovery from mammalian total cellular proteins

Serum autoantibody profiles are unique to individuals and reflect the level and history of autoimmunity and tumor immunity. The identification of autoantibody biomarkers is critical for the development of immune monitoring systems for immune-related disorders. Here, we present a practical method for large-scale autoantibody discovery using total cellular proteins from cultured mammalian cells. We found that nucleic acid-free and fully denatured water-soluble total cellular proteins from mammalian cells were superior, allowing precise separation by reversed-phase HPLC after preparing a large set of homogeneous total cellular proteins. After separating the proteins based on hydrophobicity, the fractionated samples were subjected to molecular mass analysis using conventional SDS-PAGE. The resulting two-dimensional gel electrophoresis was successfully employed for immune blotting and LC-MS/MS analysis. All procedures, including TRIzol-based total cellular protein extraction, solubilization of denatured proteins, reversed-phase HPLC separation, and SDS-PAGE, were highly reproducible and easily scalable. We propose this novel two-dimensional gel electrophoresis system as an alternative proteomics-based methodology suitable for large-scale autoantibody discovery.

"Conducted Properly, Published Incorrectly": The Evolving Status of Gel Electrophoresis Images Along Instrumental Transformations in Times of Reproducibility Crisis

For the last ten years, within molecular life sciences, the reproducibility crisis discourse has been embodied as a crisis of trust in scientific images. Beyond the contentious perception of "questionable research practices" associated with a digital turn in the production of images, this paper highlights the transformations of gel electrophoresis as a family of experimental techniques. Our aim is to analyze the evolving epistemic status of generated images and its connection with a crisis of trust in images within that field. From the 1980s to the 2000s, we identify two key innovations (precast gels and gel docs) leading to a "two-tiered" gel electrophoresis with different standardization procedures, different epistemic statuses of the produced images and different ways of generating (dis)trust in images. The first tier, exemplified by differential gel electrophoresis (DIGE), is characterized by specialized devices processing images as quantitative data. The second tier, exemplified by polyacrylamide gel electrophoresis (PAGE), is described as a routine technique making use of image as qualitative "virtual witnessing." The difference between these two tiers is particularly apparent in the ways images are processed, even though both tiers involve image digitization. Our account thus highlights different views on reproducibility within the two tiers. Comparability of images is insisted upon in the first tier while traceability is expected in the second tier. It is striking that these differences occur not only within the same scientific field, but even within the same family of experimental techniques. In the second tier, digitization entails distrust, whereas it implies a collective sentiment of trust in the first tier.

A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection

Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques' orthogonality with their different contents of data output to elucidate biological questions.

Lipidomics and proteomics: An integrative approach for early diagnosis of dementia and Alzheimer's disease

Alzheimer's disease (AD) is the most common neurodegenerative disorder and considered to be responsible for majority of worldwide prevalent dementia cases. The number of patients suffering from dementia are estimated to increase up to 115.4 million cases worldwide in 2050. Hence, AD is contemplated to be one of the major healthcare challenge in current era. This disorder is characterized by impairment in various signaling molecules at cellular and nuclear level including aggregation of Aβ protein, tau hyper phosphorylation altered lipid metabolism, metabolites dysregulation, protein intensity alteration etc. Being heterogeneous and multifactorial in nature, the disease do not has any cure or any confirmed diagnosis before the onset of clinical manifestations. Hence, there is a requisite for early diagnosis of AD in order to downturn the progression/risk of the disorder and utilization of newer technologies developed in this field are aimed to provide an extraordinary assistance towards the same. The lipidomics and proteomics constitute large scale study of cellular lipids and proteomes in biological matrices at normal stage or any stage of a disease. The study involves high throughput quantification and detection techniques such as mass spectrometry, liquid chromatography, nuclear mass resonance spectroscopy, fluorescence spectroscopy etc. The early detection of altered levels of lipids and proteins in blood or any other biological matrices could aid in preventing the progression of AD and dementia. Therefore, the present review is designed to focus on the recent techniques and early diagnostic criteria for AD, revealing the role of lipids and proteins in this disease and their assessment through different techniques.

Protein Digestion for 2D-DIGE Analysis

In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and their isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, destaining, reduction and alkylation (for silver-stained gels), and dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.

DIGE Analysis of Clinical Specimens

Two-dimensional difference gel electrophoresis (2D-DIGE) is an elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2D-GE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The use of an internal pooled standard makes 2D-DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. Technical limitations of this technique (i.e., underrating of low abundant, high molecular mass and integral membrane proteins) are counterbalanced by the incomparable separation power which allows proteoforms and unknown PTM (posttranslational modification) identification. Moreover, the image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.

Subcellular Fractionation for DIGE-Based Proteomics

Mass spectrometry-based protein methodologies have revolutionized the field of analytical biochemistry and enable the identification of hundreds to thousands of proteins in biological fluids, cell lines, and tissue. This methodology requires the initial separation of a protein constellation, and this has been successfully achieved using gel-based techniques, particularly that of fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). However, given the complexity of the proteome, fractionation techniques may be required to optimize the detection of low-abundance proteins, which are often underrepresented but which may represent important players in health and disease. Such subcellular fractionation protocols typically utilize density-gradient centrifugation and have enabled the enrichment of crude microsomes, the cytosol, the plasmalemma, the nuclei, and the mitochondria. In this chapter, we describe the experimental steps involved in the enrichment of crude microsomes from the skeletal muscle using differential centrifugation and subsequent verification of enrichment by gel electrophoresis and immunoblotting, prior to comparative 2D-DIGE analysis.

Sometimes faster can be better: Microneedling IPG strips enables higher throughput for integrative top-down proteomics

Passive rehydration of immobilized pH gradient (IPG) strips for two-dimensional gel electrophoresis (2DE) has, to our knowledge, never been quantitatively evaluated to determine an ideal rehydration time. Seeking to increase throughput without sacrificing analytical rigor, we report that a substantially shorter rehydration time is accomplished when surface area of IPG strips is increased via microneedling. Rehydration for 4 h, post microneedling, provides comparable results to overnight rehydration in final analyses by 2DE, while also shortening the overall protocol by 1 day.

The utility of molecularly imprinted polymers for mass spectrometric protein and proteomics analysis

Selective and efficient sample clean-up is important in mass spectrometric protein- and proteomics analyses from biological matrices. Molecularly imprinted polymers (MIPs), polymers prepared to have tailor-made cavities for capture of target analytes may by such represent an interesting alternative for selective clean-up. The present review aims to give an overview of the utility of MIPs for protein capture from biological matrices prior to mass spectrometry (MS) analysis. The application of MIPs in depletion of abundant proteins, in protein and proteotypic peptide capture as well as in capture of post-translational modifications (PTMs) is described and discussed. In addition, an overview of available MIP formats and their advantages and challenges is given, together with an overview of the mass spectrometric techniques used in protein analysis after MIP capture. Overall, the present literature demonstrates that for many applications MIPs for sample clean-up in mass spectrometric protein and proteomics analysis from biological matrices is still not fully matured. MIPs for proteotypic peptide capture is the most mature approach and a method for routine use may be available within the next few years.

Application of Mass Spectrometry-Based Proteomics to Barley Research

Barley (Hordeum vulgare) is the fourth most cultivated crop in the world in terms of production volume, and it is also the most important raw material of the malting and brewing industries. Barley belongs to the grass (Poaceae) family and plays an important role in food security and food safety for both humans and livestock. With the global population set to reach 9.7 billion by 2050, but with less available and/or suitable land for agriculture, the use of biotechnology tools in breeding programs are of considerable importance in the quest to meet the growing food gap. Proteomics as a member of the "omics" technologies has become popular for the investigation of proteins in cereal crops and particularly barley and its related products such as malt and beer. This technology has been applied to study how proteins in barley respond to adverse environmental conditions including abiotic and/or biotic stresses, how they are impacted during food processing including malting and brewing, and the presence of proteins implicated in celiac disease. Moreover, proteomics can be used in the future to inform breeding programs that aim to enhance the nutritional value and broaden the application of this crop in new food and beverage products. Mass spectrometry analysis is a valuable tool that, along with genomics and transcriptomics, can inform plant breeding strategies that aim to produce superior barley varieties. In this review, recent studies employing both qualitative and quantitative mass spectrometry approaches are explored with a focus on their application in cultivation, manufacturing, processing, quality, and the safety of barley and its related products.

IPC 2.0: prediction of isoelectric point and pKa dissociation constants

The isoelectric point is the pH at which a particular molecule is electrically neutral due to the equilibrium of positive and negative charges. In proteins and peptides, this depends on the dissociation constant (pK_a) of charged groups of seven amino acids and NH⁺ and COO⁻ groups at polypeptide termini. Information regarding isoelectric point and pK_a is extensively used in two-dimensional gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), crystallisation, and mass spectrometry. Therefore, there is a strong need for the in silico prediction of isoelectric point and pK_a values. In this paper, I present Isoelectric Point Calculator 2.0 (IPC 2.0), a web server for the prediction of isoelectric points and pK_a values using a mixture of deep learning and support vector regression models. The prediction accuracy (RMSD) of IPC 2.0 for proteins and peptides outperforms previous algorithms: 0.848 versus 0.868 and 0.222 versus 0.405, respectively. Moreover, the IPC 2.0 prediction of pK_a using sequence information alone was better than the prediction from structure-based methods (0.576 versus 0.826) and a few folds faster. The IPC 2.0 webserver is freely available at www.ipc2-isoelectric-point.org

Proteomics: A Tool to Study Platelet Function

Platelets are components of the blood that are highly reactive, and they quickly respond to multiple physiological and pathophysiological processes. In the last decade, it became clear that platelets are the key components of circulation, linking hemostasis, innate, and acquired immunity. Protein composition, localization, and activity are crucial for platelet function and regulation. The current state of mass spectrometry-based proteomics has tremendous potential to identify and quantify thousands of proteins from a minimal amount of material, unravel multiple post-translational modifications, and monitor platelet activity during drug treatments. This review focuses on the role of proteomics in understanding the molecular basics of the classical and newly emerging functions of platelets. including the recently described role of platelets in immunology and the development of COVID-19.The state-of-the-art proteomic technologies and their application in studying platelet biogenesis, signaling, and storage are described, and the potential of newly appeared trapped ion mobility spectrometry (TIMS) is highlighted. Additionally, implementing proteomic methods in platelet transfusion medicine, and as a diagnostic and prognostic tool, is discussed.

Omics analyses in keratoconus: from transcriptomics to proteomics

Purpose of Review

To summarize the recent advances in transcriptomics and proteomics studies of keratoconus using advanced genome-wide gene and protein expression profiling techniques.

Recent Findings

Second-generation sequencing including RNA sequencing has been widely used to characterize the genome-wide gene expression in corneal tissues or cells affected by keratoconus. Due to different sample types, sequencing platforms, and analysis pipeline, different lists of genes have been identified to be differentially expressed in KC-affected samples. Gene ontology and pathway/network analyses have indicated the involvement of genes related with extracellular matrix, WNT-signaling, TGFβ pathway, and NRF2-regulated network. High throughput proteomics studies using mass spectrometry have uncovered many KC-related protein molecules in pathways related with cytoskeleton, cell matrix, TGFβ signaling, and extracellular matrix remodeling, consistent with gene expression profiling.

Summary

Both transcriptomics and proteomics studies using genome-wide gene/protein expression profiling techniques have identified significant genes/proteins that may contribute to the pathogenesis of keratoconus. These molecules may be involved in functional categories related with extracellular matrix and TGFβ signaling. It is necessary to perform comprehensive gene/protein expression studies using larger sample size, same type of samples, up-to-date platform and bioinformatics tools.

Proteome Analysis with Classical 2D-PAGE

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is based on the combination of two orthogonal separation techniques. In the first dimension, proteins are separated by their isoelectric point, a technique known as isoelectric focusing (IEF). There are two important variants of IEF, which are carrier-ampholine (CA)-based IEF and immobilized pH-gradient (IPG)-based IEF. In the second dimension, proteins are further separated by their electrophoretic mobility using SDS-PAGE. Finally, proteins can be visualized and quantified by different staining procedures such as Coomassie, silver staining, or fluorescence labeling. This article gives detailed protocols for 2D-PAGE, using both CA- and IPG-based separation in the first dimension.

The Journey Is the Reward, a Taoist Proverb: John B. Fenn Award for Distinguished Contribution in Mass Spectrometry Lecture

This account provided by John Yates describes his incredible path as a scientist, emphasizing key decisions along the way that shaped his career and led to his landmark contributions to the field of mass spectrometry. Although perhaps best known is the development of the SEQUEST algorithm for automated interpretation of tandem mass spectra of peptides, John's achievements have spanned the field of proteomics and had major impact on the ability to address and solve significant biological problems.

Empowering Shotgun Mass Spectrometry with 2DE: A HepG2 Study

One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to catalog and annotate a myriad of heterogeneous proteoforms, produced by ca. 20 thousand genes. To achieve a detailed and personalized understanding into proteomes, we suggest using a customized RNA-seq library of potential proteoforms, which includes aberrant variants specific to certain biological samples. Two-dimensional electrophoresis coupled with high-performance liquid chromatography allowed us to downgrade the difficulty of biological mixing following shotgun mass spectrometry. To benchmark the proposed pipeline, we examined heterogeneity of the HepG2 hepatoblastoma cell line proteome. Data are available via ProteomeXchange with identifier PXD018450.

Two-Dimensional Difference Gel Electrophoresis: A Gel-Based Proteomic Approach for Protein Analysis

Two-dimensional difference gel electrophoresis (2D-DIGE) remains to be one of the most popular and versatile methods of protein separation among many proteomics technologies. Similar to traditional two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the proteins are separated based on their charges and molecular weight by 2D-DIGE. Different from 2D-PAGE, proteins are pre-labeled with different fluorescent dyes, and different protein samples are run in one gel by this method. Therefore, 2D-DIGE not only carries the advantages of 2D-PAGE but also eliminates gel-to-gel variation and achieves high resolution, sensitivity, and reproducibility.

Innovating the Concept and Practice of Two-Dimensional Gel Electrophoresis in the Analysis of Proteomes at the Proteoform Level

Two-dimensional gel electrophoresis (2DE) is an important and well-established technical platform enabling extensive top-down proteomic analysis. However, the long-held but now largely outdated conventional concepts of 2DE have clearly impacted its application to in-depth investigations of proteomes at the level of protein species/proteoforms. It is time to popularize a new concept of 2DE for proteomics. With the development and enrichment of the proteome concept, any given “protein” is now recognized to consist of a series of proteoforms. Thus, it is the proteoform, rather than the canonical protein, that is the basic unit of a proteome, and each proteoform has a specific isoelectric point (pI) and relative mass (M_r). Accordingly, using 2DE, each proteoform can routinely be resolved and arrayed according to its different pI and M_r. Each detectable spot contains multiple proteoforms derived from the same gene, as well as from different genes. Proteoforms derived from the same gene are distributed into different spots in a 2DE pattern. High-resolution 2DE is thus actually an initial level of separation to address proteome complexity and is effectively a pre-fractionation method prior to analysis using mass spectrometry (MS). Furthermore, stable isotope-labeled 2DE coupled with high-sensitivity liquid chromatography-tandem MS (LC-MS/MS) has tremendous potential for the large-scale detection, identification, and quantification of the proteoforms that constitute proteomes.

Two-Dimensional Difference Gel Electrophoresis

Two-dimensional difference gel electrophoresis (2D DIGE) is a modified form of 2D electrophoresis (2D E) that allows one to compare two or three protein samples simultaneously on the same gel. The proteins in each sample are covalently tagged with different color fluorescent dyes that are designed to have no effect on the relative migration of proteins during electrophoresis. Proteins that are common to the samples appear as "spots" with a fixed ratio of fluorescent signals, whereas proteins that differ between the samples have different fluorescence ratios. With conventional imaging systems, DIGE is capable of reliably detecting as little as 0.2 fmol of protein, and protein differences down to ± 15%, over a ~10,000-fold protein concentration range. DIGE combined with digital image analysis therefore greatly improves the statistical assessment of proteome variation. Here we describe a protocol for conducting DIGE experiments, which takes 2-3 days to complete. We have further improved upon 2D DIGE by introducing in-gel equilibration to improve protein retention during transfer between the first and second dimensions of electrophoresis and by developing a fluorescent gel imaging system with a millionfold dynamic range.

Detection and Identification of Low-Abundant Proteins Using HPE Gels, Fluorescent Stains, and MALDI-ToF-ToF-MS

Two-dimensional electrophoresis as a complementary approach to gel-free proteomic methods possesses the ability to separate physiologically important isoforms of proteins in an unbiased manner. Frequently, those isoforms are low-abundant regulators, and therefore, detection and identification of low-abundant proteins is highly necessary to exploit this advantage. We describe an experimental sequence of classical operations to process gels but optimized them, in order to identify each detectable protein spot on gel.

Application of Extracellular Vesicles Proteomics to Cardiovascular Disease: Guidelines, Data Analysis, and Future Perspectives

Extracellular vesicles (EVs) are a heterogeneous population of vesicles composed of a lipid bilayer that carry a large repertoire of molecules including proteins, lipids, and nucleic acids. In this review, some guidelines for plasma-derived EVs isolation, characterization, and proteomic analysis, and the application of the above to cardiovascular disease (CVD) studies are provided. For EVs analysis, blood samples should be collected using a 21-gauge needle, preferably in citrate tubes, and plasma stored for up to 1 year at -80°, using a single freeze-thaw cycle. For proteomic applications, differential centrifugation (including ultracentrifugation steps) is a good option for EVs isolation. EVs characterization is done by transmission electron microscopy, particle enumeration techniques (nanoparticle-tracking analysis, dynamic light scattering), and flow cytometry. Regarding the proteomics strategy, a label-free and gel-free quantitative method is a good choice due to its accuracy and because it minimizes the amount of sample required for clinical applications. Besides the above, main EVs proteomic findings in cardiovascular-related diseases are presented and analyzed in this review, paying especial attention to overlapping results between studies. The latter might offer new insights into the clinical relevance and potential of novel EVs biomarkers identified to date in the context of CVD.

Two-Dimensional Gel Electrophoresis by Glass Tube-Based IEF and SDS-PAGE

The genome information combined with data derived from modern mass spectrometry enables us to determine the identity of a protein once it is isolated from a complex mixture. Two-dimensional gel electrophoresis established more than four decades ago serves as a powerful protocol to isolate many proteins at once for such protein analysis. In the first two decades, the original procedure to use a glass tube-based IEF had been commonly used. Since an IEF in glass tubes is rather difficult to maneuver, a new method to use an IEF on a thin agarose slab backed by a plastic film (IPG Dry Strip) had been invented and is now widely used. In this chapter, we describe a protocol that uses a glass tube-based IEF because the capacity of protein loading and resolving power of this type of classic two-dimensional gel is still indispensable for many applications, not only for protein identification but also for protocols that are benefited by larger amounts of materials, i.e., analysis of posttranslational modification of proteins such as phosphorylation, methylation, glycosylation, and others.

Gel-based proteomics in disease research: Is it still valuable?

Gel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations including liquid chromatography and ionization techniques, resulting gel-free proteomics finally becoming dominant players at present. There are numerous advantages in gel-free approach in aspects of current trends of disease research. Interestingly, gel-free approaches are still advanced, it seems that gel electrophoresis will not be disappeared. The unique features of gel electrophoresis can be complementary for gel-free and it is suitable for the new wave of top-down functional proteomics.

Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review

Various methods and specialized software programs are available for processing two-dimensional gel electrophoresis (2-DGE) images. However, due to the anomalies present in these images, a reliable, automated, and highly reproducible system for 2-DGE image analysis has still not been achieved. The most common anomalies found in 2-DGE images include vertical and horizontal streaking, fuzzy spots, and background noise, which greatly complicate computational analysis. In this paper, we review the preprocessing techniques applied to 2-DGE images for noise reduction, intensity normalization, and background correction. We also present a quantitative comparison of non-linear filtering techniques applied to synthetic gel images, through analyzing the performance of the filters under specific conditions. Synthetic proteins were modeled into a two-dimensional Gaussian distribution with adjustable parameters for changing the size, intensity, and degradation. Three types of noise were added to the images: Gaussian, Rayleigh, and exponential, with signal-to-noise ratios (SNRs) ranging 8-20 decibels (dB). We compared the performance of wavelet, contourlet, total variation (TV), and wavelet-total variation (WTTV) techniques using parameters SNR and spot efficiency. In terms of spot efficiency, contourlet and TV were more sensitive to noise than wavelet and WTTV. Wavelet worked the best for images with SNR ranging 10-20 dB, whereas WTTV performed better with high noise levels. Wavelet also presented the best performance with any level of Gaussian noise and low levels (20-14 dB) of Rayleigh and exponential noise in terms of SNR. Finally, the performance of the non-linear filtering techniques was evaluated using a real 2-DGE image with previously identified proteins marked. Wavelet achieved the best detection rate for the real image.

DIGE Analysis of Human Tissues

Two-dimensional difference gel electrophoresis (2-D DIGE) is an advanced and elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2-DE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The two-dye or three-dye systems can be adopted and their choice depends on specific applications. Furthermore, the use of an internal pooled standard makes 2-D DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. The image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.

Protein Digestion for DIGE Analysis

In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence difference gel electrophoresis (DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and protein isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, de-staining, reduction and alkylation (for silver-stained gels), dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.

[Multiomics study of HepG2 cell line proteome]

Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome. We suggested multiomics approach, which combines transcriptomic (RNAseq) and proteomic (2DE-MS/MS) methods, as a promising strategy to explore the proteome.

Application of proteomics in the elucidation of chemical-mediated allergic contact dermatitis

Allergic contact dermatitis (ACD) is a widespread hypersensitivity reaction of the skin. The cellular mechanisms underlying its development are complex and involve close interaction of different cell types of the immune system. It is this very complexity which has long prevented straightforward replacement of the corresponding regulatory in vivo tests. Recent efforts have already resulted in the development of several in vitro testing alternatives that address key steps of ACD. Yet identification of suitable biomarkers is still a subject of intense research. Search strategies for the latter encompass transcriptomics, proteomics as well as metabolomics approaches. The scope of this review shall be the application and use of proteomics in the context of ACD. This includes highlighting relevant aspects of the molecular and cellular mechanisms underlying ACD, the exploitation of these mechanisms for testing and biomarkers (e.g., in the context of the OECD's adverse outcome pathway initiative) as well as an outlook on emerging proteome targets, for example during the allergen-induced activation of dendritic cells (DCs).

Recent advances in capillary ultrahigh pressure liquid chromatography

In the twenty years since its initial demonstration, capillary ultrahigh pressure liquid chromatography (UHPLC) has proven to be one of most powerful separation techniques for the analysis of complex mixtures. This review focuses on the most recent advances made since 2010 towards increasing the performance of such separations. Improvements in capillary column preparation techniques that have led to columns with unprecedented performance are described. New stationary phases and phase supports that have been reported over the past decade are detailed, with a focus on their use in capillary formats. A discussion on the instrument developments that have been required to ensure that extra-column effects do not diminish the intrinsic efficiency of these columns during analysis is also included. Finally, the impact of these capillary UHPLC topics on the field of proteomics and ways in which capillary UHPLC may continue to be applied to the separation of complex samples are addressed.

Integrating Pharmacoproteomics into Early-Phase Clinical Development: State-of-the-Art, Challenges, and Recommendations

Pharmacoproteomics is the study of disease-modifying and toxicity parameters associated with therapeutic drug administration, using analysis of quantitative and temporal changes to specific, predetermined, and select proteins, or to the proteome as a whole. Pharmacoproteomics is a rapidly evolving field, with progress in analytic technologies enabling processing of complex interactions of large number of unique proteins and effective use in clinical trials. Nevertheless, our analysis of clinicaltrials.gov and PubMed shows that the application of proteomics in early-phase clinical development is minimal and limited to few therapeutic areas, with oncology predominating. We review the history, technologies, current usage, challenges, and potential for future use, and conclude with recommendations for integration of pharmacoproteomic in early-phase drug development.

Separation of charge-regulated polyelectrolytes by pH-assisted diffusiophoresis

The potential of separating colloidal particles through pH-assisted diffusiophoresis is evaluated.

Methods for Proteome Analysis of Campylobacter jejuni Using 2-D Electrophoresis

This chapter describes protocols used for two-dimensional electrophoretic analysis of the proteome or subproteome of Campylobacter jejuni, a major human food-borne pathogen. The following protocols, adapted to Campylobacter strains, include all the steps from cultivation to gel-support protein separation.

Using titanium complexes to defeat cancer: the view from the shoulders of titans

Seeking ‘unifying mechanisms of action’ in titanium anti-cancer agents: a 40 year odyssey.

A glimpse into the modulation of post-translational modifications of human-colonizing bacteria

Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health. Herein, we address this issue by carrying out the largest and most comprehensive global pooling and comparison of PTM peptides and proteins from bacterial species performed to date. Data was collected from 91 studies relating to PTM bacterial peptides or proteins identified by mass spectrometry-based methods. The present analysis revealed that there was a considerable overlap between PTMs across species, especially between acetylation and other PTMs, particularly succinylation. Phylogenetically closer species may present more overlapping phosphoproteomes, but environmental triggers also contribute to this proximity. PTMs among bacteria were found to be extremely versatile and diverse, meaning that the same protein may undergo a wide variety of different modifications across several species, but it could also suffer different modifications within the same species.

Towards the Full Realization of 2DE Power

Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology.

Proteome-pI: proteome isoelectric point database

Proteome-pI is an online database containing information about predicted isoelectric points for 5029 proteomes calculated using 18 methods. The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques, especially for 2D gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography–mass spectrometry and X-ray protein crystallography. The database, available at http://isoelectricpointdb.org allows the retrieval of virtual 2D-PAGE plots and the development of customised fractions of proteome based on isoelectric point and molecular weight. Moreover, Proteome-pI facilitates statistical comparisons of the various prediction methods as well as biological investigation of protein isoelectric point space in all kingdoms of life. For instance, using Proteome-pI data, it is clear that Eukaryotes, which evolved tight control of homeostasis, encode proteins with pI values near the cell pH. In contrast, Archaea living frequently in extreme environments can possess proteins with a wide range of isoelectric points. The database includes various statistics and tools for interactive browsing, searching and sorting. Apart from data for individual proteomes, datasets corresponding to major protein databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr) database have also been precalculated and made available in CSV format.

IPC - Isoelectric Point Calculator

BACKGROUND

Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, pI estimation can be helpful during protein crystallization trials.

RESULTS

Here, I present the Isoelectric Point Calculator (IPC), a web service and a standalone program for the accurate estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including two new computationally optimized pKa sets. According to the presented benchmarks, the newly developed IPC pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Moreover, the prediction of pI using the IPC pKa's leads to fewer outliers, i.e., predictions affected by errors greater than a given threshold.

CONCLUSIONS

The IPC service is freely available at http://isoelectric.ovh.org Peptide and protein datasets used in the study and the precalculated pI for the PDB and some of the most frequently used proteomes are available for large-scale analysis and future development.

REVIEWERS

This article was reviewed by Frank Eisenhaber and Zoltán Gáspári.