Reappraisal of Aß40 and Aß42 Peptides Measurements in Cerebrospinal Fluid of Patients with Alzheimer's Disease.

Cerebrospinal fluid (CSF) biomarkers are currently included in the diagnostic criteria for Alzheimer's disease (AD), in particular, decreased concentrations of amyloid-ß peptide 1-42 (Aß42) in the CSF, coupled with increased levels of tau and phosphorylated tau proteins, are supportive of AD diagnosis. To date, the quantification of Aß42 levels with antibody-dependent immunoassay shows a marked variability among different laboratories and is also affected by different pre-analytical factors, suggesting that part of Aß42 peptides might be aggregated and thus undetected by antibodies. To bypass an antibody-dependent measurement, we determined the Aß40 and Aß42 levels by immunoblot. We analyzed CSF samples from 35 patients with clinical diagnosis of probable AD and from 15 age-matched normal controls; CSF Aß levels were determined by two different ELISA kits and by immunoblot analysis. Aß40 levels measured by ELISA were comparable to those obtained by immunoblot, whereas CSF concentrations of Aß42 measured by ELISA were significantly lower compared to values obtained by immunoblot quantification. Biochemical analysis, following 1D- and 2D-PAGE analysis, showed that the qualitative composition of Aß peptides in the CSF is similar in AD and controls but different from that of AD brain tissues. Moreover, sedimentation velocity in sucrose gradient of CSF and brain homogenate from AD demonstrated that Aß42 in CSF is different from Aß42 in brain in terms of solubility and aggregation state.

[Correction of the electrophoretic shift in virtual 2D SDS-PAGE electrophoresis]. / Korrektsiia élektroforeticheskogo sdviga v virtual'nom 2D SDS-PAGE élektroforeze.

Virtual electrophoresis in proteomics can be used to search localization of proteins and their proteoforms (especially those existing in low concentrations), to identify proteoforms found in experiments etc. Although the problem of predicting the isoelectric point is well studied, the need of electrophoretic shift correction is usually ignored. Researchers simply use the brutto molecular weight of the protein. In this study four data sets taken from the literature sources and the SWISS-2DPAGE database have been used to build correction equations for prediction of the electrophoretic shift (123, 72, 118 and 470 points, respectively). Two groups of models were built. The first model was based on the amino acid composition of proteins, the second one, on analysis of parameters calculated by amino acid sequences (theoretical molecular weight, hydrophobicity, charge distribution, ability to form helix structures). The coefficient of determination ranged from 0.35 to 0.75 in each single set, but cross-prediction between samples did not gave satisfactory results. At the same time, the direction of correction was predicted correctly in 74% of cases. After combining of the samples and dividing pooled data into 2 representative sets, the coefficient of determination during in the process of learning ranged from 0.44 to 0.51, and R2 of predictions were not less than 0.39. The direction of correction was predicted correctly in 80% of cases. This prediction models have been integrated into the program pIPredict v.2, freely available at http://www.ibmc.msk.ru/LPCIT/pIPredict.

2-DE combined with two-layer feature selection accurately establishes the origin of oolong tea.

Taiwan is known for its high quality oolong tea. Because of high consumer demand, some tea manufactures mix lower quality leaves with genuine Taiwan oolong tea in order to increase profits. Robust scientific methods are, therefore, needed to verify the origin and quality of tea leaves. In this study, we investigated whether two-dimensional gel electrophoresis (2-DE) and nanoscale liquid chromatography/tandem mass spectroscopy (nano-LC/MS/MS) coupled with a two-layer feature selection mechanism comprising information gain attribute evaluation (IGAE) and support vector machine feature selection (SVM-FS) are useful in identifying characteristic proteins that can be used as markers of the original source of oolong tea. Samples in this study included oolong tea leaves from 23 different sources. We found that our method had an accuracy of 95.5% in correctly identifying the origin of the leaves. Overall, our method is a novel approach for determining the origin of oolong tea leaves.

Two-dimensional gel-based protein standardization verified by western blot analysis.

In data presentation of biochemical investigation the amount of a target protein is shown in the y-axis against the x-axis representing time, concentrations of various agents, or other parameters. Western blot is a versatile and convenient tool in such an analysis to quantify and display the amount of proteins. In western blot, so-called housekeeping gene product(s), or "housekeeping proteins," are widely used as internal standards. The rationale of using housekeeping proteins for standardization of western blot is based on the assumption that the expression of chosen housekeeping gene is always constant, which could be false under certain physiological or pathological conditions. We have devised a two-dimensional gel-based standardization method in which the protein content of each sample is determined by scanning the total protein density of two-dimensional gels and the expression of each protein is quantified as the density ratio of each protein divided by the density of the total proteins on the two-dimensional gel. The advantage of this standardization method is that it is not based on any presumed "housekeeping proteins" that are supposed to be being expressed constantly under all physiological conditions. We will show that the total density of a two-dimensional gel can render a reliable protein standardization parameter by running western blot analysis on one of the proteins analyzed by two-dimensional gels.

Higher sensitivity of capillary electrophoresis in detecting hemoglobin A2'compared to traditional gel electrophoresis.

HbA2' (also called Hb B2) is the most common delta-globin chain defect and is reported to occur in 1-2% of the African American population. The major clinical significance of HbA2' is that the failure to detect it might lead to an underestimation of the total HbA2, leading to failure to diagnose ß-thalassemia minor. In order to diagnose ß-thalassemia minor, both HbA2 and HbA2' levels must be combined.Hb A2' accounts for a small percentage (1-2%) of the total hemoglobin in heterozygotes. It is difficult to detect this small amount by traditional gel electrophoresis. Using HPLC Hb A2' is easily detected as it produces a minor peak in the S window. Other conditions which might interfere with detection of HbA2' by HPLC include Hb S trait or Hb SS disease (Hb A2' hidden in the S peak), transfused Hb SS (Hb S peak may be very small), Hb C trait or Hb CC disease (glycosylated Hb C elutes in the S window), and Hb G (Hb G2 elutes in the S window). All of the above conditions, including Hb A2', occur most commonly in the same ethnic group (African American). We reviewed 654 consecutive cases over a period of three months for the presence of Hb A2' in our laboratory where capillary electrophoresis is used as the primary diagnostic tool. We detected seven cases (1.07 %) of HbA2'. In contrast, we did not detect any HbA2' using conventional gel electrophoresis in the last one year (2,580 cases). Although in none of the seven cases the sum of Hb A2 and Hb A2' exceeded 3.5%, we believe that capillary electrophoresis allows for a better detection of Hb A2' than gel electrophoresis and HPLC.

Quality control and stability studies with the monoclonal antibody, trastuzumab: application of 1D- vs. 2D-gel electrophoresis.

Recombinant monoclonal antibodies (rmAbs) are medicinal products obtained by rDNA technology. Consequently, like other biopharmaceuticals, they require the extensive and rigorous characterization of the quality attributes, such as identity, structural integrity, purity and stability. The aim of this work was to study the suitability of gel electrophoresis for the assessment of charge heterogeneity, post-translational modifications and the stability of the therapeutic, recombinant monoclonal antibody, trastuzumab. One-dimensional, SDS-PAGE, under reducing and non-reducing conditions, and two-dimensional gel electrophoresis were used for the determination of molecular mass (Mr), the isoelectric point (pI), charge-related isoform patterns and the stability of trastuzumab, subjected to stressed degradation and long-term conditions. For the assessment of the influence of glycosylation in the charge heterogeneity pattern of trastuzumab, an enzymatic deglycosylation study has been performed using N-glycosidase F and sialidase, whereas carboxypeptidase B was used for the lysine truncation study. Experimental data documented that 1D and 2D gel electrophoresis represent fast and easy methods to evaluate the quality of biological medicinal products. Important stability parameters, such as the protein aggregation, can be assessed, as well.

2D-ToGo workflow: increasing feasibility and reproducibility of 2-dimensional gel electrophoresis.

Two-dimensional gel electrophoresis (2-DE) is one of the most powerful methods for studying global protein profiles. However, due to the multiple manual steps involved in gel based processing it is challenging to achieve the necessary overall reproducibility for a reliable comparative analysis, especially between different laboratories. To improve the 2-DE technique for quantitative analyses we have set up a robust 2-DE workflow, called 2D-ToGo, which utilizes latest innovations concerning instrumentation, consumables and protocols. Quantitative data analyses indicate the high reproducibility between replicate gels processed at a single site (intra-laboratory variation: CV 20%). The data-sets of the inter-laboratory comparison revealed similar results displaying a variation of CV 23%. The technical improvements given by our 2-DE workflow have a positive impact on process robustness and most importantly, reproducibility. Accordingly, many of the well-known challenges for resolving and quantitating up to thousands of different protein components in a given biological sample are minimized.

Improved proteomic analysis of nuclear proteins, as exemplified by the comparison of two myeloid cell lines nuclear proteomes.

One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in the organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear acids. Several experimental procedures have been tested to increase, in the nuclear extract, the ratio of nuclear proteins compared to contaminant proteins, and also to obtain reproducible conditions compatible with 2D-gel electrophoresis. The NaCl procedure has been chosen. To test the interest of this procedure, the nuclear protein expression profiles of macrophages and dendritic cells have been compared with a proteomic approach by 2D-gel electrophoresis. Delta2D software and mass spectrometry analyses have allowed pointing out some proteins of interest. We have chosen some of them, involved in transcriptional regulation and/or chromatin structure for further validations. The immunoblotting experiments have shown that most of the observed changes are due to post-translational modifications, thereby exemplifying the interest of the 2D gel approach. Finally, this approach allowed us to reach not only high abundance nuclear proteins but also lower abundance proteins, such as the HP1 proteins and reinforces the interest of using 2DE-gel in proteomics because of its ability to visualize intact proteins with their modifications.

Leukocyte p53 protein biosignature through standard-aligned two-dimensional immunoblotting.

Peripheral leukocytes may reflect systemic disease and stress states through their gene expression profile. Subsequent protein analyses of leukocytes are hypothesized to provide essential information regarding systemic diseases. We have developed a protein biosignature analysis of the tumour suppressor and cell stress sensor p53 based on two-dimensional gel electrophoresis and immunoblotting, and utilize fluorescently labelled reference standards to significantly improve the alignment and comparison of biosignatures, including full-length p53 and isoforms p53ß and p53γ. Analysis of the p53 biosignatures of peripheral blood mononuclear cells from 526 healthy individuals and 65 acute myeloid leukaemia patients indicated a novel putative p53 protein variant in a subset of individuals (227 of 526 healthy tested). The p53 variant was more distinct in the reference standard aligned biosignatures of healthy individuals, compared to the non-standard aligned leukaemia biosignatures. This approximately 2 kDa heavier variant of p53 appeared with similar frequency in leukemic and healthy test persons, without coinciding with known splice forms or post-translational modifications of p53. We propose that a standardized leukocyte protein biosignature of p53 provides a powerful research tool and indicate how p53 protein biosignatures may be used in future diagnostics. This article is part of a Special Issue entitled: Integrated omics.

Silver staining of 2D electrophoresis gels.

Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It -combines excellent sensitivity (in the low nanogram range) with the use of very simple and cheap equipment and chemicals. For its use in proteomics, two important additional features must be considered, compatibility with mass spectrometry and quantitative response. Both features are discussed in this chapter, and optimized silver staining protocols are proposed.

Two-dimensional gel electrophoresis: vertical isoelectric focusing.

Two-dimensional gel electrophoresis (2-DE) is one of the most powerful tools for separating proteins based on their size and charge. 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 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.

Counterion dye staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and tryptic gel digestion of stained protein for mass spectrometry.

A fast and matrix-assisted laser desorption/ionization mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon and ethyl violet, to form an ion-pair complex. The protocol, including fixing, staining, and quick washing steps, can be completed in 1-1.5 h, depending upon gel thickness. It has the sensitivity comparable to the colloidal Coomassie Brilliant Blue G stain using phosphoric acid as a component of staining solution (4-8 ng). The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from mass spectrometry. Considering the speed, sensitivity, and compatibility with mass spectrometry, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.

TEMED-enhanced photoluminescent imaging of human serum proteins by quantum dots after PAGE.

Polyacrylamide gel electrophoresis (PAGE) has been one of the most powerful and widely used separation techniques for complex biological samples, whose traditional detection methods include organic dye or silver staining. As a simple, convenient, and ultrasensitive detection of proteins for PAGE, a novel enhanced photoluminescent (PL) imaging method was developed. Thioglycolic acid (TGA)-capped CdTe quantum dots (QDs) and the enhanced reagent of tetramethylethylenediamine (TEMED) are introduced, achieving the direct detection of various proteins in native 1-DE, 2-DE, and SDS gels. Here, we describe the general protocol of TEMED-enhanced PL imaging by QDs, including materials, practical procedures, as well as some notes.

The challenge to quantify proteins with charge trains due to isoforms or conformers.

Single proteins separated by 2-DE often show multiple spots spreading along the first dimension. In many cases, such charge trains are explained by isoform differences or by putative post-translational modifications including phosphorylation, glycosylation and others. We now report that individual spots of such charge trains on 2-D gels in fact often represent the same protein, but, apparently due to conformational changes, segregate to different isoelectric points. If MS analysis reveals protein identity, we therefore suggest integrating all individual spots within a charge train for quantification. Especially in quality control of pharmaceutical proteins, the integration of the spot groups of all active contents is preferable in order to obtain reproducible and reasonable quantitative results. However, most commercial software packages for gel analysis integrate the signals spot-wise. We provide an improved quantification tool for proteins with charge train groups. This calculation can be implemented using the MATLAB software and the self-developed "Correct Integration Software System" or the commercial software package Delta2D.

Statistical issues in quality control of proteomic analyses: good experimental design and planning.

Quality control is becoming increasingly important in proteomic investigations as experiments become more multivariate and quantitative. Quality control applies to all stages of an investigation and statistics can play a key role. In this review, the role of statistical ideas in the design and planning of an investigation is described. This involves the design of unbiased experiments using key concepts from statistical experimental design, the understanding of the biological and analytical variation in a system using variance components analysis and the determination of a required sample size to perform a statistically powerful investigation. These concepts are described through simple examples and an example data set from a 2-D DIGE pilot experiment. Each of these concepts can prove useful in producing better and more reproducible data.

Data variance and statistical significance in 2D-gel electrophoresis and DIGE experiments: comparison of the effects of normalization methods.

Identifying changes in the relative abundance of proteins between different biological samples is often confounded by technical noise. In this work, we compared eight normalization methods commonly used in two-dimensional gel electrophoresis and difference gel electrophoresis (DIGE) experiments for their ability to reduce noise and for their influence on the list of proteins whose difference in abundance between two samples is determined to be statistically significant. With respect to reducing noise we find that, while all methods improve upon unnormalized data, cyclic linear normalization is the least well suited to gel-based proteomics and the performances of the other methods are similar. We also find in DIGE data that the choice of normalization method has less of an impact on the noise than does the decision to use an internal reference in the experimental design and that both normalization and standardization using the internal reference are required to maximally reduce variance. Despite the similar noise reduction achieved by most normalization methods, the list of proteins whose abundance was determined to differ significantly between biological groups differed depending on the choice of normalization method. This work provides a direct comparison of the impact of normalization methods in the context of common experimental designs.

A methodical approach for improving the reliability of quantifiable two-dimensional Western blots.

Western transfer after the electrophoretic separation of proteins onto an adsorbent membrane, with subsequent immunodetection, is a powerful tool for detecting and characterizing a multitude of proteins. An important aspect of the study of proteins is that they often exist as isoforms with structural microheterogeneity giving rise to differences in biological activity. Western blotting (WB) in combination with two-dimensional SDS-polyacrylamide gel electrophoresis (2D-SDS-PAGE) allows the specific quantification of single isoforms of a protein. We have investigated whether a methodical modification of 2D-SDS-PAGE improves the quality of quantifiable 2D-WB data. The effect of a combined separation of three previously electrofocused protein extracts lying side by side on a single SDS-gel in parallel has been tested against the traditional procedure, viz., the separation of one protein extract per SDS-gel. The modified procedure results in a more reliable and better quality data than the traditional procedure, which seems to be prone to producing systematic or random errors. Our simple practical procedure improves immunoblotting accuracy by excluding numerous sources of errors and saves time, immunoblotting reagents and costly antibodies.

Quantitative erythrocyte membrane proteome analysis with Blue-native/SDS PAGE.

The erythrocyte membrane plays a pivotal role in erythrocyte functioning. Many membrane protein aberrations are known that result in hemolytic anemia, however, the origin of numerous disorders is not known to date. To extend the current set of diagnostic tools, we used a novel proteome-wide approach to quantitatively analyze membrane proteins of healthy donor and patient erythrocytes. Blue-native PAGE has proven to be a powerful tool for separation of membrane proteins and their complexes, but has hitherto not been applied to erythrocyte membranes to find biomarkers. Using this technique, we detected almost 150 protein spots, from which more than 500 proteins could be identified by LC-MS/MS. Further, we successfully assessed the potential of using CyDye labeling to quantify the membrane proteins. Our final goal was to determine if this approach is suited to detect protein level changes in disordered erythrocyte membranes, and we could successfully confirm that erythrocyte spectrin levels were dramatically decreased for a hemolytic anemia patient. This approach provides a new tool to detect potential biomarkers and can contribute to an improved understanding of the causes of erythrocyte membrane defects in patients suffering from hemolytic anemia.