NullCanada: A novel α1-antitrypsin allele with in cis variants Glu366Lys and Ile100Asn

BACKGROUND

α₁-Antitrypsin (A1AT) deficiency predisposes patients to pulmonary disease due to inadequate protection against human neutrophil elastase released during inflammatory responses. A1AT deficiency is caused by homozygosity or compound heterozygosity for A1AT variants; individuals with A1AT deficiency most commonly have at least one Z variant allele (c.1096G > A (Glu366Lys)). Null variants that result in complete absence of A1AT in the plasma are much rarer. With one recent exception, all reported A1AT variants are characterized by a single pathogenic variant.

CASE

An 8 years old patient from Edmonton, Alberta, Canada, was investigated for A1AT deficiency. His A1AT phenotype was determined to be M (wild type)/Null by isoelectric focusing (IEF) but M/Z by targeted genotyping. Gene sequencing revealed two heterozygous variants: Z and Ile100Asn (c.299 T > A). The Ile100Asn substitution is predicted to disrupt the secondary structure of an α-helix in which it resides and the neighbouring tertiary structure, resulting in intracellular degradation of A1AT prior to hepatocyte secretion.

METHODS

Family testing was conducted to verify potential inheritance of an A1AT allele carrying the two mutations in cis, as this arrangement of the mutations would explain "Z" detection by genotyping but not by IEF. Molecular modeling was used to assess the effect of the variants on A1AT structure and stability.

DISCUSSION

Carrier status for a novel variant Null_Canada with in cis mutations (c.[299 T > A;1096G > A], p.[(Ileu100Asn;Glu366Lys)]) was confirmed. A sibling was identified as having A1AT deficiency on the basis of compound heterozygosity for two alleles: Null_Canada and the common Z allele. A separate pedigree from the Maritimes was subsequently recognized as carrying Null_Canada.

CONCLUSION

In cis mutations such as Null_Canada may be more common than previously described due to failure to detect such mutations using historical testing methods. Combined approaches that include gene sequencing and segregation studies allow recognition of rare A1AT variants, including in cis mutations.

Evaluation of a semi-automatic isoelectric focusing method for apolipoprotein E phenotyping

A qualitative, semi-automatized method for apolipoprotein E (apoE) phenotyping by isoelectric focusing method has been evaluated on 40 serum samples from patients previously genotyped for apoE, especially as regards concordance with genotyping, but also repeatability and reproducibility of the method, and sample storage. Total concordance with genotyping and good precision criteria, together with its practicability and requirement of a little sample volume, lead to conclude to the usefulness of this method to help clinicians in the diagnosis of dyslipidemic and neurodegenerative diseases.

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Semi-automatic isoelectrofocusing method for apoE phenotyping.

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Total concordance with genotyping.

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Good repeatability and reproducibility.

A facile isoelectric focusing of myoglobin and hemoglobin used as markers for screening of chicken meat quality in China

A novel analytical protocol was developed for general quality screening of chicken meat based on IEF and protein extraction. To demonstrate the developed protocol, 24 chickens were divided into three groups; each had eight chickens. The chickens in Group 1 were slaughtered by exsanguination, Group 2 asphyxiated in water, and that in Group 3 were infected by new castle disease virus. Proteins were extracted from the meat samples by using pure water as an extractant, separated by IEF, verified by western blot, and quantified via imaging analysis. The relevant experiments demonstrated that two myoglobin (Mb) bands were detected at pI 6.8 and 7.04 for all samples of Groups 1, 2, and 3, but there were additional hemoglobin (Hb) bands at pI 7.09 and 7.13 (P < 0.05) for the samples of Groups 2 and 3. The results implied that Hb bands might be a potential biomarker for the screening of chicken meat quality. The RSD values of two Mb bands (pI 6.8 and 7.04) in Group 1 were respectively 4.08 and 3.63%, the ones of two Hb bands (pI 7.09 and 7.13) in Group 2 were 3.66 and 2.10%, and those in Group 3 were 2.17% and 2.77%, respectively. All the RSD values indicated high stability and reliability of the developed protocol. Additionally, the protocol had a direct readout of protein bands in IEF without staining. However, it was time-consuming and had high cost. Even so, the relevant general method and finding have potential for screening of chicken meat quality.

Comparative charge-based separation study with various capillary electrophoresis (CE) modes and cation exchange chromatography (CEX) for the analysis of monoclonal antibodies

Charge heterogeneity is an important critical quality attribute for the analysis of monoclonal antibodies (mAbs). For this, (imaged) capillary isoelectric focusing ((i)cIEF), ion exchange chromatography (IEC) and, recently, capillary zone electrophoresis (CZE) are the predominantly used techniques. In order to investigate which one is most suitable to answer a specific analytical question, here, the four aforementioned separation techniques were systematically evaluated using NISTmAb and Infliximab as test molecules. The performance parameters (precision, separation efficiency, linearity and sensitivity) were determined under comparable conditions. Moreover, important aspects for daily routine such as speed and ease of use were considered. Each technique has its own pros and cons. The (i)cIEF methodology is distinguished by its excellent separation efficiency. In addition, the native fluorescence mode in icIEF is a good tool to analyze small sample amounts (LOQ: 2.8 mg/l for Infliximab). Nevertheless, high performance liquid chromatography (HPLC) still has superior precision. CZE, and also micellar electrokinetic chromatography (MEKC), have emerged as further interesting alternatives. For all techniques, variations connected to the sample preparation strongly influence precision. Looking at the relative standard deviation (RSD) values of the relative peak areas, all techniques provide acceptable performance (RSD: 0.6-1.6%).

Carrier ampholyte-free free-flow isoelectric focusing for separation of protein

Free-flow isoelectric focusing (FFIEF) has the merits of mild separation conditions, high recovery and resolution, but suffers from the issues of ampholytes interference and high cost due to expensive carrier ampholytes. In this paper, a home-made carrier ampholyte-free FFIEF system was constructed via orientated migration of H⁺ and OH^- provided by electrode solutions. When applying an electric field, a linear pH gradient from pH 4 to 9 (R² = 0.994) was automatically formed by the electromigration of protons and hydroxyl ions in the separation chamber. The carrier ampholyte-free FFIEF system not only avoids interference of ampholyte to detection but also guarantees high separation resolution by establishing stable pH gradient. The separation selectivity was conveniently adjusted by controlling operating voltage and optimizing the composition, concentration and flow rate of the carrier buffer. The constructed system was applied to separation of proteins in egg white, followed by MADLI-TOF-MS identification. Three major proteins, ovomucoid, ovalbumin and ovotransferrin, were successfully separated according to their pI values with 15 mmol/L Tris-acetic acid (pH = 6.5) as carrier buffer at a flow rate of 12.9 mL/min.

Transferrin glycosylation analysis from dried blood spot cards and capillary blood samples

BACKGROUND

Congenital disorders of glycosylation (CDG) are a growing group of inherited diseases causing manifold symptoms. Routine diagnostic procedures are high performance liquid chromatography (HPLC) or isoelectric focusing (IEF) of serum transferrin.

METHODS

We introduce a modified method to screen for glycosylation abnormalities from dried blood spot (DBS) samples based on isoelectric focusing. In PGM1-CDG, glycosylation analysis and enzyme activity measurement were performed from a single DBS sample. Furthermore, we present the possibility to use capillary blood samples for quantification of transferrin isoforms.

RESULTS

IEF from DBS samples is possible and results are identical to the ones obtained in serum samples. Gel analysis using the ImageJ software allows quantification of IEF results. Storage at -20 °C ensures stable samples for more than six months. Capillary blood samples are equally suitable for glycosylation analysis and show no inferiority to serum samples.

CONCLUSION

In view of a growing number of treatable CDG subtypes, the proposed methods allow reliable diagnosis and therapy control of CDG while being easily applicable. Capillary blood samples can be taken at home and sent in for follow-up. DBS are widely used in new-born screening programs and have the potential to broaden the knowledge of glycosylation abnormalities in early infancy. By its possible application in the context of alcohol abuse, the proposed method bears the potential for widespread use in a non-metabolic context.

Two-Dimensional Biochemical Purification for Global Proteomic Analysis of Macromolecular Protein Complexes

A high-resolution two-dimensional (2-D) proteomic fractionation technique for the systematic purification and subsequent mass spectrometry-based identification of endogenous protein macromolecular complexes is described. The method hyphenates preparative isoelectric focusing (IEF) with mixed-bed ion exchange chromatography (IEX) to efficiently separate cell- or tissue- derived soluble protein mixtures, allowing for more effective and less biased physiochemical characterization of stable multiprotein assemblies. After comprehensive 2D fractionation of cell-free lysates, each fraction is subjected to quantitative tandem mass spectrometry (MS/MS) and subsequent computational analysis to map high-confidence protein-protein interactions (PPIs). Herein, the experimental component (workflow protocols) for this global "interactome" network mapping platform is described.

Introduction to Protein Electrophoresis

This chapter briefly discusses the developments in electrophoresis of proteins from Tiselius' moving-boundary electrophoresis to the modern-day two-dimensional polyacrylamide gel electrophoresis. It also touches upon the staining methods used to visualize total proteins post electrophoresis.

Two-Dimensional Electrophoresis and Mass Spectrometry for Protein Identification

Two-dimensional electrophoresis is useful for separation of individual proteins that can be easily isolated and processed with mass spectrometry for their identification. Here we describe a simplified method of 2D electrophoresis with aim to help beginners in optimization of protein separation protocol, which can be further modified to enhance protein spot resolution. Current protocol can be used in different fields of biology including progenitor cells.

Two-Dimensional Gel Electrophoresis with Immobilized pH Gradients

Isoelectric focusing (IEF) is a technique in protein research that has been used since 1975 to separate proteins based on their isoelectric point. When combined with sodium dodecyl sulfate polyacrylamide gel electrophoresis, this procedure allows for high-resolution separation of cellular proteins for analytical purposes. Laboratories perform IEF by (a) using carrier ampholytes that migrate through a gel to create the pH gradient or (b) using immobilized pH gradients (IPG) that contain ampholytes bound covalently to a gel. Here we describe an IEF system that uses immobilized pH gradient (IPG) strips that undergo the desired current and voltage setting to separate proteins based on its charge in the first dimension followed by SDS PAGE to generate a two-dimensional map of serum proteins.

Microfluidic Free-Flow Isoelectric Focusing with Real-Time pI Determination

Free-flow electrophoresis (FFE) may be used for continuous and preparative separation of a wide variety of biomolecules. Isoelectric focusing (IEF) provides for the separation of compounds according to their isoelectric point (pI). Here we describe a microfluidic chip-based protocol for the fabrication, application, and optical monitoring of free-flow isoelectric focusing (FFIEF) of proteins and peptides on the microscale with optical surveillance of the microscopic pH gradient provided by an integrated pH sensing layer. This protocol may be used with modifications also for the FFIEF of other biomolecules and may serve as template for the fabrication of microfluidic chips with integrated fluorescent or luminescent pH sensor layers for FFE and other applications.

Two-Dimensional Gel Electrophoresis: Vertical Isoelectric Focusing

Two-dimensional gel electrophoresis is one of the most powerful tools for separating proteins based on their size and charge. Two-dimensional gel electrophoresis (2-DE) is very useful to separate two proteins with identical molecular weights but different charges, which cannot be achieved with just sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Here, a simpler and easier version of 2-DE is presented which is also faster than all the currently available techniques. In this modified version of 2-DE, isoelectric focusing is carried out in the first dimension using a vertical sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) apparatus. Following the first-dimensional IEF, each individual lane is excised from the IEF gel and after a 90° rotation, is inserted into a second-dimensional SDS-PAGE, which can be stained with Coomassie Brilliant Blue for protein analysis or immunoblotted for further analysis. This version of IEF can be run in less than 2 h compared to the overnight run required by O'Farrell's method. Difficult tube gel casting and gel extrusion as well as tube gel distortion are eliminated in our method. This method is simpler, faster, and inexpensive. Both dimensions can be done on the same SDS-PAGE apparatus, and up to ten samples can be run simultaneously using one gel.

Single-Cell High-Resolution Detection and Quantification of Protein Isoforms Differing by a Single Charge Unit

Isoelectric focusing (IEF) is an electrophoretic technique that enables the separation of proteins based on their isoelectric points. Until recently, this valuable method was not feasible for single-cell applications, which are necessary to interrogate heterogeneous cell populations. Herein we highlight a recently published method enabling the analysis of single-cell proteomics, which utilizes microfluidics coupled with IEF, photocapture, and immunoprobing of the protein in the same micro-gel, which can be stripped and reprobed multiple times.

Immunofixation Electrophoresis for Identification of Proteins and Specific Antibodies

Immunofixation electrophoresis (IFE) is a technique for the identification of proteins within complex mixtures after separation by either conventional zone electrophoresis or isoelectric focusing. Most commonly antigens (which are often immunoglobulins) are separated by electrophoresis followed by precipitation with specific antibodies in situ. However, immunoglobulins with specific reactivity can be also precipitated with the proper antigens after electrophoresis in reverse or reversed IFE. Because of its great versatility, potentially high sensitivity, ease to perform and customize, and relatively low cost with no requirement for expensive instrumentation, manual IFE remains a valuable tool for both clinical diagnostic testing and research. Any low-viscosity body fluid specimen or, possibly, culture fluid could be tested with IFE if proper antibodies (or antigens in reverse[d] IFE) are available. After pretreatment with chaotropic and/or reducing agents, even high-viscosity specimens might be amenable to testing with IFE.

Muscarinic receptor antagonists activate ERK-CREB signaling to augment neurite outgrowth of adult sensory neurons

A major cellular effector activated by G protein coupled receptors is extracellular signal-regulated kinase (ERK). The ERK signaling cascade regulates a variety of cellular processes including growth and proliferation. Both G protein and β-arrestin-mediated signaling lead to ERK activation by phosphorylation through different kinases. Recently, we have shown muscarinic acetylcholine type 1 receptor (M₁R) antagonists, muscarinic toxin 7 (MT7) and pirenzepine, elevated neurite outgrowth and protected from small and large fiber neuropathy in adult sensory neurons in various animal models. Thus, we tested the novel hypothesis that muscarinic antagonists could drive neurite outgrowth through altered M₁R-ERK signaling. We have used two dimensional isoelectric focusing/SDS-PAGE combined with analysis using multiple phospho-epitope specific antibodies to study ERK1/2 phosphorylation and activation of its downstream nuclear effector cyclic response element binding protein (CREB). Activated CREB is known to exhibit neuroprotective and growth promoting effects. One hour of treatment with MT7 and pirenzepine activated ERK through M₁R and induced a significant increase in levels of pCREB(S133) in cultured sensory neurons. Further, pharmacological blockade or siRNA based knockdown of ERK abolished the MT7 and pirenzepine mediated neuritogenic effect. In addition, we have shown drug-induced alterations of charged protein fractions that may possess additional post-translationally modified forms of ERK and CREB. For the first time we show that long-term treatment, e.g. 1 h, with muscarinic antagonists selective or specific for M₁R can activate a biased β-arrestin dependent ERK-CREB signal cascade. Our study gives novel insight into muscarinic antagonist-mediated modulation of M₁R-ERK-CREB signaling which could be exploited for therapy in neuropathic diseases.

Cerebrospinal fluid analysis and the determination of oligoclonal bands

This document presents the guidelines for the cerebrospinal fluid (CSF) analysis and the determination of oligoclonal bands (OCBs) as pivotal tests in neuroinflammatory pathologies of the central nervous system. The guidelines have been developed following a consensus process built on questionnaire-based surveys, internet contacts, and discussions at workshops of the sponsoring Italian Association of Neuroimmunology (AINI) congresses. Essential clinical information on the pathologies in which the CSF analysis is indicated, and, particularly, on those characterized by the presence of OCBs in the intrathecal compartment, indications and limits of CSF analysis and OCB determination, instructions for result interpretation, and agreed laboratory protocols (Appendix) are reported for the communicative community of neurologists and clinical pathologists.

Evaluation of semi-automatic image analysis tools for cerebrospinal fluid electrophoresis of IgG oligoclonal bands

Background

IgG concentrations in cerebrospinal fluid generally range from 20 to 45 mg/L. In multiple sclerosis immune reactions lead to intrathecal synthesis of specific IgGs that can be detected in biological fluid samples both quantitatively and qualitatively by isoelectric focusing of supplementary oligoclonal IgG bands.

Method

A simple tool, using the MATLAB application, to facilitate and improve isoelectric focusing profile analysis is presented and evaluated in terms of its sensitivity, repeatability and reproducibility. A comparison between human readers and semi-automatic method has also been performed.

Results

Results from the semi-automatic method were found to be equivalent or superior to generally employed laboratory methods. Repeatability analysis for semi-automatic processing yielded coefficients of variation (CVs) in the 3–7% range, and using a sample with an estimated IgG concentration of 200 mg/L, four bands were still visible after dilution to 5 mg/L, corresponding to band concentrations of 1.1–1.6 mg/L. Discordances between visual inspection and automatic analysis only appear at threshold levels for interpretation (the gray zone).

Conclusion

The semi-automatic method has acceptable performance for routine implementation.

Correlating charge heterogeneity data generated by agarose gel isoelectric focusing and ion exchange chromatography methods

An isoelectric focusing method (IEF) has been used to assess the charge heterogeneity profile of a monoclonal antibody during the early stages of product development. A more precise and sensitive ion exchange chromatography (IEC/CEX) method was developed and implemented as development progressed and was used concurrently with IEF for lot release and to monitor charge heterogeneity. Charge variants resolved by both methods (IEC and IEF) were purified and characterized. Tryptic peptide mapping and N- linked oligosaccharide profile analyses of the IEC and IEF fractions indicated a structural correlation between the charge variants separated by these two methods. The major sources of molecular heterogeneity were due to the variation in the sialyated carbohydrate structure and heavy chain C-terminal lysine truncation. By monitoring the rates of change in the charge heterogeneity profiles of the monoclonal antibody stored at elevated temperatures by the IEC and IEF methods, a positive correlation between the two methods was established. This approach enabled replacement of the IEF method with the more precise IEC method.

Proteomic Analysis of Non-model Plant Tissues Using Phenol Extraction, Two-Dimensional Electrophoresis, and MALDI Mass Spectrometry

Separation of plant proteins by means of electrophoretic techniques is quite challenging since different compounds typical for plant cells can interfere and/or reduce the effectiveness of the protein isolation. This is particularly problematic for two-dimensional electrophoresis (2-DE). Therefore, it is important to optimize protein extraction and to establish a robust protocol for 2-DE and downstream processing, primarily mass spectrometry (MS) analysis. Here we give a detailed protocol for protein extraction using phenol method, 2-DE, and MALDI-MS analysis.

Rapid 2D DIGE Proteomic Analysis of Mouse Liver

Several years have passed since LC-MS(/MS) became the mainstream for proteomic analysis; however, conventional 2D DIGE (two-dimensional difference gel electrophoresis) continues to be an important technology that enables rapid and direct visualization of hundreds to thousands of proteins and their quantitative analyses. We can get global proteomic views using 2D DIGE within 3 days, and then identify proteins with differential expression levels using MALDI-TOF/MS and MASCOT search engine within a week. Here, we describe our routine 2D DIGE proteomic analysis of the liver isolated from mice in pathological conditions.

High-resolution dynamic computer simulation of electrophoresis using a multiphysics software platform

The modeling and simulation software COMSOL Multiphysics^® was recently extended with an electrophoretic transport interface. Its performance was investigated by comparison to results obtained using the 1D dynamic electrophoresis simulators GENTRANS and SIMUL5. Simulations of zone electrophoresis, isotachophoresis, isoelectric focusing and of an oscillating electrolyte system were performed. Smooth profiles were essentially identical indicating that the COMSOL electrophoretic transport interface is able to reproduce results of the 1D simulators. Differences in the way the respective numerical schemes handle steep concentration gradients and associated instabilities were observed. The COMSOL electrophoretic transport interface is expected to be useful as a general model for simulations in 1D, 2D or 3D geometries, as well as for simulations combining electrophoresis with other physical phenomena.

Comparative Testis Tissue Proteomics Using 2-Dye Versus 3-Dye DIGE Analysis

Comparative tissue proteomics aims to analyze alterations of the proteome in response to a stimulus. Two-dimensional difference gel electrophoresis (2D-DIGE) is a modified and advanced form of 2D gel electrophoresis. DIGE is a powerful biochemical method that compares two or three protein samples on the same analytical gel, and can be used to establish differentially expressed protein levels between healthy normal and diseased pathological tissue sample groups. Minimal DIGE labeling can be used via a 2-dye system with Cy3 and Cy5 or a 3-dye system with Cy2, Cy3, and Cy5 to fluorescently label samples with CyDye flours pre-electrophoresis. DIGE circumvents gel-to-gel variability by multiplexing samples to a single gel and through the use of a pooled internal standard for normalization. This form of quantitative high-resolution proteomics facilitates the comparative analysis and evaluation of tissue protein compositions. Comparing tissue groups under different conditions is crucially important for advancing the biomedical field by characterization of cellular processes, understanding pathophysiological development and tissue biomarker discovery. This chapter discusses 2D-DIGE as a comparative tissue proteomic technique and describes in detail the experimental steps required for comparative proteomic analysis employing both options of 2-dye and 3-dye DIGE minimal labeling.

A simple method to estimate the isoelectric point of modified Tomato bushy stunt virus (TBSV) particles

We present a simple method to estimate the isoelectric point (pI) of Tomato Bushy Stunt particles. We demonstrate that the combination of agarose gels with different pH buffers can be used to electrophorese the virus particles and their migration patterns can be compared. This method allows us to estimate the pI of the virus particles (wild type, wt, and genetically modified particles) and to monitor the effect of the pI of modified peptide side chains of the viral capsid subunit on the pI of the whole virus particle.

Surface isoelectric focusing (sIEF) with carrier ampholyte pH gradient

Isoelectric focusing (IEF) is a powerful tool for amphoteric protein separations because of high sensitivity, bio-compatibility, and reduced complexity compared to chromatography or mechanical separation techniques. IEF miniaturization is attractive because it enables rapid analysis, easier adaptation to point of care applications, and smaller sample demands. However, existing small-scale IEF tools have not yet been able to analyze single protein spots from array libraries, which are ubiquitous in many pharmaceutical discovery and screening protocols. Thus, we introduce an in situ, novel, miniaturized protein analysis approach that we have termed surface isoelectric focusing (sIEF). Low volume printed sIEF gels can be run at length scales of ∼300 μm, utilize ∼0.9 ng of protein with voltages below 10 V. Further, the sIEF device platform is so simple that it can be integrated with protein library arrays to reduce cost; devices demonstrate reusability above 50 uses. An acrylamide monomer solution containing broad-range carrier ampholytes was microprinted with a Nano eNabler^TM between micropatterned gold electrodes spaced 300 μm apart on a glass slide. The acrylamide gel was polymerized in situ followed by protein loading via printed diffusional exchange. A pH gradient formed via carrier ampholyte stacking when electrodes were energized; the gradient was verified using ratiometric pH-sensitive FITC/TRITC dyes. Green fluorescent protein (GFP) and R-phycoerythrin (R-PE) were utilized both as pI markers and to test sIEF performance as a function of electric field strength and ampholyte concentration. Factors hampering sIEF included cathodic drift and pH gradient compression, but were reduced by co-printing non-ionic Synperonic® F-108 surfactant to reduce protein-gel interactions. sIEF gels achieved protein separations in <10 min yielding bands < 50 μm wide with peak capacities of ∼8 and minimum pI differences from 0.12 to 0.14. This new sIEF technique demonstrated comparable focusing at ∼100 times smaller dimensions than any previous IEF. Further, sample volumes required were reduced four orders of magnitude from 20 μL for slab gel IEF to 0.002 μL for sIEF. In summary, sIEF advantages include smaller volumes, reduced power consumption, and microchip surface accessibility to focused bands along with equivalent separation resolutions to prior IEF tools. These attributes position this new technology for rapid, in situ protein library analysis in clinical and pharmaceutical settings.

A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis

Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.