Inventory of proteoforms as a current challenge of proteomics: Some technical aspects

Puzzle of Proteoform Variety-Where Is a Key?

One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.

A Current State of Proteomics in Adult and Pediatric Inflammatory Bowel Diseases: A Systematic Search and Review

Inflammatory bowel diseases (IBD) are systemic immune-mediated conditions with predilection for the gastrointestinal tract and include Crohn's disease and ulcerative colitis. Despite the advances in the fields of basic and applied research, the etiopathogenesis remains largely unknown. As a result, only one third of the patients achieve endoscopic remission. A substantial portion of the patients also develop severe clinical complications or neoplasia. The need for novel biomarkers that can enhance diagnostic accuracy, more precisely reflect disease activity, and predict a complicated disease course, thus, remains high. Genomic and transcriptomic studies contributed substantially to our understanding of the immunopathological pathways involved in disease initiation and progression. However, eventual genomic alterations do not necessarily translate into the final clinical picture. Proteomics may represent a missing link between the genome, transcriptome, and phenotypical presentation of the disease. Based on the analysis of a large spectrum of proteins in tissues, it seems to be a promising method for the identification of new biomarkers. This systematic search and review summarize the current state of proteomics in human IBD. It comments on the utility of proteomics in research, describes the basic proteomic techniques, and provides an up-to-date overview of available studies in both adult and pediatric IBD.

Optimized Proteome Reduction for Integrative Top–Down Proteomics

Integrative top–down proteomics is an analytical approach that fully addresses the breadth and complexity needed for effective and routine assessment of proteomes. Nonetheless, any such assessments also require a rigorous review of methodology to ensure the deepest possible quantitative proteome analyses. Here, we establish an optimized general protocol for proteome extracts to improve the reduction of proteoforms and, thus, resolution in 2DE. Dithiothreitol (DTT), tributylphosphine (TBP), and 2-hydroxyethyldisulfide (HED), combined and alone, were tested in one-dimensional SDS-PAGE (1DE), prior to implementation into a full 2DE protocol. Prior to sample rehydration, reduction with 100 mM DTT + 5 mM TBP yielded increased spot counts, total signal, and spot circularity (i.e., decreased streaking) compared to other conditions and reduction protocols reported in the literature. The data indicate that many widely implemented reduction protocols are significantly ‘under-powered’ in terms of proteoform reduction and thus, limit the quality and depth of routine top–down proteomic analyses.

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.

Proteomic and lipidomic biomarkers in the diagnosis and progression of inflammatory bowel disease - a review

PURPOSE

There is an increasing prevalence of inflammatory bowel disease (IBD) and to date, no effective treatment has been developed and the exact etiology of this disease remains unknown. Nevertheless, a growing number of proteomic and lipidomic studies have identified certain proteins and lipids which can be used successfully in patients to improve diagnoses and monitoring of treatment.

EXPERIMENTAL DESIGN

We have focused on the applications of proteins and lipids for IBD diagnostics, including differentiation of Crohn's disease (CD) and ulcerative colitis (UC), treatment monitoring, monitoring of clinical state, likelihood of relapse, and their potential for novel targeted treatments.

RESULTS

Analysis of protein and lipid profiles can: improve the availability and use of diagnostic markers; improve understanding of the pathomechanisms of IBD, for example, several studies have implicated platelet dysfunction (PF4), autoimmune responses (granzyme B, perforin), and abnormal metabolism (arachidonic acid pathways); aid in monitoring patient health; and improve therapeutics (experimental phosphatidylcholine therapy has been shown to result in an improvement in intestinal condition).

CONCLUSIONS

Despite the enormous progress of proteomics and lipidomics in recent years and the development of new technologies, further research is needed to select some of the most sensitive and specific markers applicable in diagnosing and treating IBD.

Accurate Proteoform Identification and Quantitation Using pTop 2.0

The remarkable advancement of top-down proteomics in the past decade is driven by the technological development in separation, mass spectrometry (MS) instrumentation, novel fragmentation, and bioinformatics. However, the accurate identification and quantification of proteoforms, all clearly-defined molecular forms of protein products from a single gene, remain a challenging computational task. This is in part due to the complicated mass spectra from intact proteoforms when compared to those from the digested peptides. Herein, pTop 2.0 is developed to fill in the gap between the large-scale complex top-down MS data and the shortage of high-accuracy bioinformatic tools. Compared with pTop 1.0, the first version, pTop 2.0 concentrates mainly on the identification of the proteoforms with unexpected modifications or a terminal truncation. The quantitation based on isotopic labeling is also a new function, which can be carried out by the convenient and user-friendly "one-key operation," integrated together with the qualitative identifications. The accuracy and running speed of pTop 2.0 is significantly improved on the test data sets. This chapter will introduce the main features, step-by-step running operations, and algorithmic developments of pTop 2.0 in order to push the identification and quantitation of intact proteoforms to a higher-accuracy level in top-down proteomics.

Proteomes Are of Proteoforms: Embracing the Complexity

Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?

Omics: The way forward to enhance abiotic stress tolerance in Brassica napus L

Plant abiotic stresses negative affects growth and development, causing a massive reduction in global agricultural production. Rapeseed (Brassica napus L.) is a major oilseed crop because of its economic value and oilseed production. However, its productivity has been reduced by many environmental adversities. Therefore, it is a prime need to grow rapeseed cultivars, which can withstand numerous abiotic stresses. To understand the various molecular and cellular mechanisms underlying the abiotic stress tolerance and improvement in rapeseed, omics approaches have been extensively employed in recent years. This review summarized the recent advancement in genomics, transcriptomics, proteomics, metabolomics, and their imploration in abiotic stress regulation in rapeseed. Some persisting bottlenecks have been highlighted, demanding proper attention to fully explore the omics tools. Further, the potential prospects of the CRISPR/Cas9 system for genome editing to assist molecular breeding in developing abiotic stress-tolerant rapeseed genotypes have also been explained. In short, the combination of integrated omics, genome editing, and speed breeding can alter rapeseed production worldwide.

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.

A database for inventory of proteoform profiles: "2DE-pattern"

The human proteome is composed of a diverse and heterogeneous range of gene products/proteoforms/protein species. Because of the growing amount of information about proteoforms generated by different methods, we need a convenient approach to make an inventory of the data. Here, we present a database of proteoforms that is based on information obtained by separation of proteoforms using 2DE followed by shotgun ESI-LC-MS/MS. The database's principles and structure are described. The database is called "2DE-pattern" as it contains multiple isoform-centric patterns of proteoforms separated according to 2DE principles. The database can be freely used at http://2de-pattern.pnpi.nrcki.ru.

What Is New in (Plant) Proteomics Methods and Protocols: The 2015-2019 Quinquennium

The third edition of "Plant Proteomics Methods and Protocols," with the title "Advances in Proteomics Techniques, Data Validation, and Integration with Other Classic and -Omics Approaches in the Systems Biology Direction," was conceived as being based on the success of the previous editions, and the continuous advances and improvements in proteomic techniques, equipment, and bioinformatics tools, and their uses in basic and translational plant biology research that has occurred in the past 5 years (in round figures, of around 22,000 publications referenced in WoS, 2000 were devoted to plants).The monograph contains 29 chapters with detailed proteomics protocols commonly employed in plant biology research. They present recent advances at all workflow stages, starting from the laboratory (tissue and cell fractionation, protein extraction, depletion, purification, separation, MS analysis, quantification) and ending on the computer (algorithms for protein identification and quantification, bioinformatics tools for data analysis, databases and repositories). At the end of each chapter there are enough explanatory notes and comments to make the protocols easily applicable to other biological systems and/or studies, discussing limitations, artifacts, or pitfalls. For that reason, as with the previous editions, it would be especially useful for beginners or novices.Out of the 29 chapters, six are devoted to descriptive proteomics, with a special emphasis on subcellular protein profiling (Chapters 5 - 10 ), six to PTMs (Chapters 11 , and 14 - 18 ), three to protein interactions (Chapters 19 - 21 ), and two to specific proteins, peroxidases (Chapter 24 ) and proteases and protease inhibitors (Chapter 26 ). The book reflects the new trajectory in MS-based protein identification and quantification, moving from the classic gel-based approaches to the most recent labeling (Chapters 10 , 11 , 29 ), shotgun (Chapters 5 , 7 , 12 , 15 ), parallel reaction monitoring (Chapter 16 ), and targeted data acquisition (Chapter 13 ). MS imaging (Chapter 25 ), the only in vivo MS-based proteomics strategy, is far from being fully optimized and exploited in plant biology research. A confident protein identification and quantitation, especially in orphan species, of low-abundance proteins, is still a challenging task (Chapters 4 , 28 ).What is really new is the use of different techniques for proteomics data validation and their integration into other classic and -omics approaches in the systems biology direction. Chapter 2 reports on multiple extractions in a single experiment of the different biomolecules, nucleic acids, proteins, and metabolites. Chapter 27 describes how metabolic pathways can be reconstructed from multiple -omics data, and Chapter 3 network building. Finally, Chapters 22 and 23 deal with, respectively, the search for allele-specific proteins and proteogenomics.Around 200 groups were, almost 1 year ago, invited to take part in this edition. Unfortunately, only 10% of them kindly accepted. My gratitude to those who accepted our invitation but also to those who did not, as all of them have contributed to the plant proteomics field. I will enlist, in this introductory chapter, following my own judgment, some of the relevant papers published in the past 5 years, those that have shown us how to enhance and exploit the potential of proteomics in plant biology research, without aiming at giving a too exhaustive list.

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.

Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium

This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the "dark part" of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.

Unbiased Thiol-Labeling and Top-Down Proteomic Analyses Implicate Multiple Proteins in the Late Steps of Regulated Secretion

Regulated exocytosis enables temporal and spatial control over the secretion of biologically active compounds; however, the mechanism by which Ca²⁺ modulates different stages of exocytosis is still poorly understood. For an unbiased, top-down proteomic approach, select thiol- reactive reagents were used to investigate this process in release-ready native secretory vesicles. We previously characterized a biphasic effect of these reagents on Ca²⁺-triggered exocytosis: low doses potentiated Ca²⁺ sensitivity, whereas high doses inhibited Ca²⁺ sensitivity and extent of vesicle fusion. Capitalizing on this novel potentiating effect, we have now identified fluorescent thiol- reactive reagents producing the same effects: Lucifer yellow iodoacetamide, monobromobimane, and dibromobimane. Top-down proteomic analyses of fluorescently labeled proteins from total and cholesterol-enriched vesicle membrane fractions using two-dimensional gel electrophoresis coupled with mass spectrometry identified several candidate targets, some of which have been previously linked to the late steps of regulated exocytosis and some of which are novel. Initial validation studies indicate that Rab proteins are involved in the modulation of Ca²⁺ sensitivity, and thus the efficiency of membrane fusion, which may, in part, be linked to their previously identified upstream roles in vesicle docking.

A next generation setup for pre-fractionation of non-denatured proteins reveals diverse albumin proteoforms each carrying several post-translational modifications

Proteomic biomarker search requires the greatest analytical reproducibility and detailed information on altered proteoforms. Our protein pre-fractionation applies orthogonal native chromatography and conserves important features of protein variants such as native molecular weight, charge and major glycans. Moreover, we maximized reproducibility of sample pre-fractionation and preparation before mass spectrometry by parallelization and automation. In blood plasma and cerebrospinal fluid (CSF), most proteins, including candidate biomarkers, distribute into a multitude of chromatographic clusters. Plasma albumin, for example, divides into 15-17 clusters. As an example of our technique, we analyzed these albumin clusters from healthy volunteers and from dogs and identified cluster-typical modification patterns. Renal disease further modifies these patterns. In human CSF, we found only a subset of proteoforms with fewer modifications than in plasma. We infer from this example that our method can be used to identify and characterize distinct proteoforms and, optionally, enrich them, thereby yielding the characteristics of proteoform-selective biomarkers.

Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives

Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date. This is because the presence of a given gene mutation does not automatically correspond to changes in its expression or final metabolic or structural effect(s). Furthermore, the existence of these gene susceptibility loci in the normal population suggests other driving prerequisites for the disease manifestation. Proteins can be considered the main functional units as almost all intracellular physiological functions as well as intercellular interactions are dependent on them. Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved. Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression. This review describes the state of the art in the field with respect to the study of IBD and the potential for translation from biomarker discovery to clinical application.

Reducing Complexity? Cysteine Reduction and S-Alkylation in Proteomic Workflows: Practical Considerations

Reduction and alkylation are common processing steps in sample preparation for qualitative and quantitative proteomic analyses. In principle, these steps mitigate the limitations resulting from the presence of disulfide bridges. There has been recurring debate in the proteomics community around their use, with concern over negative impacts that result from overalkylation (off-target, non-thiol sites) or incomplete reduction and/or S-alkylation of cysteine. This chapter integrates findings from a number of studies on different reduction and alkylation strategies, to guide users in experimental design for their optimal use in proteomic workflows.

Differences in Root Physiological and Proteomic Responses to Dibutyl Phthalate Exposure between Low- and High-DBP-Accumulation Cultivars of Brassica parachinensis

Di- n-butyl phthalate (DBP), as an endocrine-disrupting chemical that tends to be accumulated in crops, poses great risks to human health through the food chain. To identify the molecular mechanism underlying differences in their DBP accumulation, the root physiological and proteomic responses to DBP stress of two Brassica parachinensis cultivars, a high-DBP accumulator (Huaguan) and a low-DBP accumulator (Lvbao), were investigated. Root damage of greater severity and significantly greater ( p < 0.05) decreases in root protein content and root activity were detected in Lvbao than in Huaguan, suggesting that Lvbao had lower tolerance to DBP. In total, 52 DBP-responsive proteins were identified by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. More proteins involved in basic metabolic processes, such as protein synthesis and energy metabolism, were downregulated in Lvbao, possibly explaining its lower tolerance and root damage. Several proteins involved in starch metabolism, cell-wall biosynthesis and modification, and stress response were activated in Huaguan, suggesting greater tolerance to DBP. Overall, differences in root proteome between the two cultivars might be responsible for the genotype-dependent DBP tolerance and accumulation in B. parachinensis.

Next Steps on in Silico 2DE Analyses of Chromosome 18 Proteoforms

In the boundaries of the chromosome-centric Human Proteome Project (c-HPP) to obtain information about proteoforms coded by chromosome 18, several cell lines (HepG2, glioblastoma, LEH), normal liver, and plasma were analyzed. In our study, we have been using proteoform separation by two-dimensional electrophoresis (2DE) (a sectional analysis) and a semivirtual 2DE with following shotgun mass spectrometry using LC-ESI-MS/MS. Previously, we published a first draft of this research, where only HepG2 cells were tested. Here, we present the next step using more detailed analysis and more samples. Altogether, confident (2 significant sequences minimum) information about proteoforms of 117 isoforms coded by 104 genes of chromosome 18 was obtained. The 3D-graphs showing distribution of different proteoforms from the same gene in the 2D map were generated. Additionally, a semivirtual 2DE approach has allowed for detecting more proteoforms and estimating their pI more precisely. Data are available via ProteomeXchange with identifier PXD010142.