Systematic evaluation of sample preparation methods for gel-based human urinary proteomics: quantity, quality, and variability

We performed systematic evaluation of 38 protocols to concentrate normal human urinary proteins prior to 2D-PAGE analysis. Recovery yield and pattern of resolved protein spots were compared among different methods and intra-/inter-individual variabilities were examined. Precipitation with 90% ethanol provided the greatest protein recovery yield (92.99%), whereas precipitation with 10% acetic acid had the least protein recovery (1.91%). In most of precipitation protocols, the higher percentage of applied organic compounds provided the greater recovery yield. With a fixed concentration at 75%, the urine precipitated with acetonitrile had the greatest number of protein spots visualized in 2D gel, whereas the acetic-precipitated sample had the smallest number of spots. For the intra-individual variability, the first morning urine had the greatest amount of total protein but provided the smallest number of protein spots visualized. Excessive water drinking, not caffeine ingestion, caused alterations in the urinary proteome profile with newly presenting spots and also proteins with decreased excretion levels. As expected, there was a considerable degree of inter-individual variability. Coefficients of variation for albumin and transferrin expression were greatest by inter-individual variables. Male urine had greater amount of total protein but provided smaller number of protein spots compared to female urine. These data offer a wealth of useful information for designing a high-quality, large-scale human urine proteome project.     

A dilution immunoassay to measure myosin regulatory light chain phosphorylation

We examined the quantitation of myosin regulatory light chain phosphorylation (MRLCP) by Western blot and found both offset and saturation errors. The desirable characteristics of an MRLCP assay are that the dynamic range be 60- to 100-fold and that the detection threshold be known and preferably very small relative to total MRLC concentration. No technique examined provided all these characteristics. However, accurate measurements can be obtained by including serial dilutions of the sample to provide a fractional calibration scale in terms of the dephosphorylated light chain and by using interpolation of the phosphorylated band signal intensity to provide values for the relative phosphorylation ratio. We found that this method offers several advantages over methods that rely on signal ratios from single samples: The dilution ratio method is less subject to errors from differences in protein load, it offers estimates of the error in the individual measurement, and has some redundancy that increases the likelihood of obtaining a valid measurement despite gel or membrane artifacts.     

Variability of urine proteome in healthy humans during a 105-day isolation in a pressurized compartment

The protein composition (proteome) of the body fluids is rather flexible; it can change, responding to various factors of the external environment and changes in the internal environment. In order to study the variability of the proteome profile in healthy humans under the conditions of total control of vital rhythm, physical activity, and diet, urine samples were collected from subjects who had been selected according to special criteria and qualified as healthy by a special physical evaluation board. The subjects took part in an experiment with a 105-day-long isolation in a pressurized compartment, carried out by using an autonomous life-support system at the Institute of Biomedical Problems, Russian Academy of Sciences. The purification and concentration of proteins from the urine samples were carried out using a MB-HIC C8 magnetic bead set (Bruker Daltonics). The mass spectra have been obtained using an Autoflex III time-of-flight mass spectrometer (Bruker Daltonics) in the positive lineal mode. One hundred and seventeen peaks were obtained for each urine sample; technological errors of the method have been studied. The high variability of the urine proteome profile (36 protein MC peaks on average) was shown in healthy humans under the conditions of isolation and controlled vital activity.     

DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA) and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR) was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF) tissues, 6 formalin-fixed paraffin-embedded (FFPE) tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard workflow for qualification of DNA preparations should include the sequential combination of NanoDrop and Qubit to assess the purity and quantity of dsDNA, respectively.     

Determination of serum protein concentration in nanoliter blood samples using fluorescamine or 9-phthalaldehyde.

Fluorometric procedures were developed to permit measurement of total protein concentration in nanoliter serum samples, using either fluorescamine or o-phthalaldehyde. The sensitivities of assays using these two reagents were similar, but the o-phthalaldehyde method was found to be somewhat simpler and more reproducible. Accurate measurements could be obtained on serum samples of 4 to 5 nl with either reagent, by using a serum standard. Fluorescence differed considerably among individual serum proteins, albumin generally showing greater fluorescence than globulins. Small molecular weight species in serum did not contribute appreciably to total serum fluorescence with either reagent.     

Development of a metabolomic approach based on urine samples and direct infusion mass spectrometry

The analysis of urine by direct infusion mass spectrometry suffers from ion suppression due to its high salt content and inter-sample variability caused by the differences in urine volume between persons. Thus, urine metabolomics requires a careful selection of the sample preparation procedure and a normalization strategy to deal with these problems. Several approaches were tested for metabolomic analysis of urine samples by direct infusion electrospray mass spectrometry (DI–ESI–MS), including solid phase extraction, liquid–liquid extraction, and sample dilution. In addition, normalization of results based on conductivity values and statistical treatment was performed to minimize sample variability. Both urine dilution and solid phase extraction with mixed mode sorbent considerably reduced the salt content in urine, providing comprehensive metabolomic fingerprints. Moreover, statistical data normalization enabled the correction of inter-sample physiological variability, improving the quality of results obtained. Therefore, high-throughput DI–ESI–MS fingerprinting of urine samples can be achieved with simple pretreatment procedures allowing the use of this noninvasive sampling in metabolomics. Finally, the optimized approach was tested in a pilot metabolomic investigation of urine samples from transgenic mice models of Alzheimer’s disease (APP/PS1) in order to illustrate the potential of the methodology.     

Assessment of reproducibility in depletion and enrichment workflows for plasma proteomics using label‐free quantitative data‐independent LC‐MS

Quantitation in plasma‐based proteomics necessitates the reproducible removal of highly abundant proteins to enable the less abundant proteins to be visible to the mass spectrometer. We have evaluated immunodepletion (proteoprep20) and enrichment (Bio‐Rad beads), as the current predominant approaches. Label‐free analysis offers an opportunity to estimate the effectiveness of this approach without incorporating chemical labels. Human plasma samples were used to quantitatively assess the reproducibility of these two methods using nano‐LC‐data‐independent acquisition MS. We have selected 18 candidate proteins and a comparison of both methodologies showed that both of the methods were reproducible and fell below 20% residual SD. With the same candidate proteins, individual inter‐day variability for the samples was also processed, allowing us to monitor instrument reproducibility. Overall, a total of 131 proteins were identified by both methods with 272 proteins identified by enrichment and 200 identified by immunodepletion. Reproducibility of measurements of the amount of protein in the processed sample for individual proteins is within analytically acceptable standards for both methodologies. This enables both methods to be used for biomarker studies. However, when sample is limited, enrichment is not suitable as larger volumes (>1.0 mL) are required. In experiments where sample is not limited then a greater number of proteins can be reliably identified using enrichment.     

Interlaboratory comparison study of serum total testoserone measurements performed by mass spectrometry methods

Background

Though mass spectrometry (MS) assays are increasingly used for routine clinical measurements of serum total testosterone (TT), information about the variability of results is limited. This study assessed the variability of TT measurement results from routine MS assays.

Methods

Twenty serum samples (12 females, 8 males) were analyzed on 2 days by seven high performance liquid chromatography (HPLC), and one gas chromatography (GC)-tandem mass spectrometry (HPLC-MS/MS, GC-MS/MS) assays. Two samples (male and female) were provided in five replicates to assess the within-run variability. Results were compared against those obtained at National Institute of Standards and Technology (NIST). The within- and between-laboratory variability was assessed for each sample. Comparisons to the NIST results were performed using bias plot and Deming regression analysis.

Results

The overall coefficient of variation of the results obtained with MS assays was <15%CV at >1.53 nmol/L and <34%CV at 0.3 nmol/L. The between-assay variability was the major contributor to the overall variability. The assay precision was the highest (<3%CV) with assays using liquid-liquid extraction for sample preparation or GC-MS/MS. The mean percent difference to the reference assay was 11%. The slopes of Deming regression analysis of the MS assays were between 0.903 and 1.138 (correlation coefficient: >0.996). TT concentrations for one assay were above the measurement range.

Conclusions

The variability of TT measurement results among MS assays is substantially smaller than that reported for immunoassays. The type of sample preparation may affect assay precision. Standardizing assays can further reduce the variability of measurement results.     

Differential sequencing with mass spectrometry

Differential or genetic sequencing requires searching sample DNA for variations with respect to a reference sequence. Conventional detection techniques are too labor and cost expensive for use in diagnostic applications, therefore new technologies will be required. Measurement techniques based on mass spectrometry (MS) possess the potential for high-throughput, high fidelity measurement of sequence variation. Unambiguous detection of polymorphic sequences has been demonstrated, even in heterozygous samples. Automated reproducible measurements of microscopic arrays of samples will enable the high-throughput detection required for large-scale applications. Computational simulation and analysis of experimental parameters prior to experimentation will provide the optimization necessary for development of robust, reproducible measurements.     

The quantitative determination of glycosaminoglycans in urine with Alcian Blue 8GX

1. The effect of MgCl(2) concentration on the interaction of Alcian Blue 8GX and glycosaminoglycans in the urine of patients with mucopolysaccharidosis was studied by using a new quantitative micro method for the measurement of Alcian Blue-glycosaminoglycan complexes. This provided a means of measuring the critical electrolyte concentrations of urinary glycosaminoglycans. 2. Theoretical considerations based on the preceding paper (Whiteman, 1973) and experimental evidence provided here show that Alcian Blue 8GX may be used for the direct quantitative determination of total urinary glycosaminoglycans. The method is simple, requires sample volumes of 50mul or less, and gives results comparable with those obtained by other more complicated methods.     

Hair analysis for opiates: evaluation of washing and incubation procedures

Hair analysis of drugs of abuse has been a subject of interest from a clinical, social and forensic perspective for years because of the broad time detection window after intake in comparison to urine or blood. However, the correct and reliable interpretation of opiates findings in an authentic hair sample requires optimalisation and standardisation of decontamination and incubation procedures. Comparing various published methods, we have found some variability in them and no unequivocal recommended procedure for starting with a method directly. Therefore, various combinations of solvents, of various polarity, as washing solvents were tested for removing opiates from the external surface of real hair samples. The yields of opiates from these washings were compared with the yields from the interior of the hair matrix after digestion with various procedures. The opiates after digestion were cleaned up from resulting solution on extraction columns with mixed solid-phase and analysed by GC–MS in standard EI mode after silylation. The efficiencies of neutral (Söerensen buffer, pH 7.4), acid (0.1 M HCl) and basic (1 M NaOH) digestion of the hair matrix were evaluated and the relative recoveries for morphine, codeine, dihydrocodeine and hydrocodone were compared. As it is very problematic to imitate the reference hair sample with a specific amount of analytes incorporated inside, which can be used for calibration to get a close estimate of the quantities of analytes inside the solid authentic sample, the total digestion of a hair sample in basic medium was considered to be a very important reference basis for quantitative determinations. The ratios of hydrolysis of labile 6-acetylmorphine or acetylcodeine were tested and evaluated in practical routine conditions of acid or neutral digestion of hair. Comparing the three methods of incubation of authentic hair samples, the methods using 1 M NaOH or 0.1 M HCl yielded higher recoveries of total equivalents of morphine or codeine, whereas the incubation in Söerensen buffer allowed the reflection of real ratios of labile metabolites and/or parent compounds in an original sample. This method has been shown to be capable of detecting hydrocodone in hair with other opiates concomitantly and to indicate the drug abuse pattern of a person at various time intervals in the past.     

Fluorometric determination of the DNA concentration in municipal drinking water

DNA concentrations in municipal drinking water samples were measured by fluorometry, using Hoechst 33258 fluorochrome. The concentration, extraction, and detection methods used were adapted from existing techniques. The method is reproducible, fast, accurate, and simple. The amounts of DNA per cell for five different bacterial isolates obtained from drinking water samples were determined by measuring DNA concentration and total cell concentration (acridine orange epifluorescence direct cell counting) in stationary pure cultures. The relationship between DNA concentration and epifluorescence total direct cell concentration in 11 different drinking water samples was linear and positive; the amounts of DNA per cell in these samples did not differ significantly from the amounts in pure culture isolates. We found significant linear correlations between DNA concentration and colony-forming unit concentration, as well as between epifluorescence direct cell counts and colony-forming unit concentration. DNA concentration measurements of municipal drinking water samples appear to monitor changes in bacteriological quality at least as well as total heterotrophic plate counting and epifluorescence direct cell counting.     

Diagnostic Accuracy of Urine Protein/Creatinine Ratio Is Influenced by Urine Concentration

Background

The usage of urine protein/creatinine ratio to estimate daily urine protein excretion is prevalent, but relatively little attention has been paid to the influence of urine concentration and its impact on test accuracy. We took advantage of 24-hour urine collection to examine both urine protein/creatinine ratio (UPCR) and daily urine protein excretion, with the latter as the reference standard. Specific gravity from a concomitant urinalysis of the same urine sample was used to indicate the urine concentration.

Methods

During 2010 to 2014, there were 540 adequately collected 24h urine samples with protein concentration, creatinine concentration, total volume, and a concomitant urinalysis of the same sample. Variables associated with an accurate UPCR estimation were determined by multivariate linear regression analysis. Receiver operating characteristic (ROC) curves were generated to determine the discriminant cut-off values of urine creatinine concentration for predicting an accurate UPCR estimation in either dilute or concentrated urine samples.

Results

Our findings indicated that for dilute urine, as indicated by a low urine specific gravity, UPCR is more likely to overestimate the actual daily urine protein excretion. On the contrary, UPCR of concentrated urine is more likely to result in an underestimation. By ROC curve analysis, the best cut-off value of urine creatinine concentration for predicting overestimation by UPCR of dilute urine (specific gravity ≦ 1.005) was ≦ 38.8 mg/dL, whereas the best cut-off values of urine creatinine for predicting underestimation by UPCR of thick urine were ≧ 63.6 mg/dL (specific gravity ≧ 1.015), ≧ 62.1 mg/dL (specific gravity ≧ 1.020), ≧ 61.5 mg/dL (specific gravity ≧ 1.025), respectively. We also compared distribution patterns of urine creatinine concentration of 24h urine cohort with a concurrent spot urine cohort and found that the underestimation might be more profound in single voided samples.

Conclusions

The UPCR in samples with low or high specific gravity is more likely to overestimate or underestimate actual daily urine protein amount, respectively, especially in a dilute urine sample with its creatinine below 38.8 mg/dL or a concentrated sample with its creatinine above 61.5 mg/dL. In particular, UPCR results should be interpreted with caution in cases that involve dilute urine samples because its overestimation may lead to an erroneous diagnosis of proteinuric renal disease or an incorrect staging of chronic kidney disease.     

Fluorometric determination of the DNA concentration in municipal drinking water.

DNA concentrations in municipal drinking water samples were measured by fluorometry, using Hoechst 33258 fluorochrome. The concentration, extraction, and detection methods used were adapted from existing techniques. The method is reproducible, fast, accurate, and simple. The amounts of DNA per cell for five different bacterial isolates obtained from drinking water samples were determined by measuring DNA concentration and total cell concentration (acridine orange epifluorescence direct cell counting) in stationary pure cultures. The relationship between DNA concentration and epifluorescence total direct cell concentration in 11 different drinking water samples was linear and positive; the amounts of DNA per cell in these samples did not differ significantly from the amounts in pure culture isolates. We found significant linear correlations between DNA concentration and colony-forming unit concentration, as well as between epifluorescence direct cell counts and colony-forming unit concentration. DNA concentration measurements of municipal drinking water samples appear to monitor changes in bacteriological quality at least as well as total heterotrophic plate counting and epifluorescence direct cell counting.     

Laboratory reporting of urine protein and albumin

Communication between pathology laboratories and clients involves more than just a result. There may be advice on recommended specimen type as well as the units and reference intervals used to report results. Between-laboratory variability in these factors has the potential to cause unnecessary confusion and even to lead to variation in interpretation for samples sent to different laboratories. A survey of Australian and New Zealand laboratories covering sample recommendations, specimens received, units and reference intervals for urine albumin and urine protein was conducted through the Royal College of Pathologists of Australasia Quality Assurance Program (RCPA QAP). The results confirm earlier findings of wide between-laboratory variability in all these factors. It is proposed that only recommendations developed by relevant professional societies and adopted by all laboratories can lead to reduction in this variability.     

Variation in protein levels obtained from human blood cells and biofluids for platelet, peripheral blood mononuclear cell, plasma, urine and saliva proteomics

Blood cells and biofluid proteomics are emerging as a valuable tool to assess effects of interventions on health and disease. This study is aimed to assess the amount and variability of proteins from platelets, peripheral blood mononuclear cells (PBMC), plasma, urine and saliva from ten healthy volunteers for proteomics analysis, and whether protein yield is affected by prolonged fasting. Volunteers provided blood, saliva and morning urine samples once a week for 4 weeks after an overnight fast. Volunteers were fasted for a further 24 h after the fourth sampling before providing their final samples. Each 10 mL whole blood provided 400–1,500 μg protein from platelets, and 100–600 μg from PBMC. 30 μL plasma depleted of albumin and IgG provided 350–650 μg protein. A sample of morning urine provided 0.9–8.6 mg protein/dL, and a sample of saliva provided 70–950 μg protein/mL. None of these yields were influenced by the degree of fasting (overnight or 36 h). In conclusion, in contrast to the yields from plasma, platelets and PBMC, the protein yields of urine and saliva samples were highly variable within and between subjects. Certain disease conditions may cause higher or lower PBMC counts and thus protein yields, or increased urinary protein levels.     

Evaluation of the double-quantum filter for the measurement of intracellular sodium concentration

Evaluation of the double-quantum filter for sodium was performed on several sample series of bovine serum albumin in water. Both single-quantum (1Q) and double-quantum (2Q) measurements were obtained. The quality of the 2Q filter was found to be quite sensitive to pulse width setting. Ordinary 1Q measurements of sodium in albumin-containing solutions show 100% visibility. At high ionic strengths, the 2Q albumin results confirm earlier conclusions demonstrating the tendency for the albumin molecule to unfold under a variety of influences. At physiological sodium concentrations, the magnitude of the 2Q/1Q ratio is controlled not only by the concentration of albumin, but also by the solution pH. Non-zero, double-quantum signals were observed in physiological samples consisting of essentially intracellular material (packed red blood cells) as well as in extracellular material (plasma and urine). Measurements in human urine showed no 2Q signal. However, high-concentration NaCl solutions did produce real, measurable 2Q signals. Therefore, the 2Q filter does not measure intracellular sodium exclusively. Although packed red blood cells gave the highest 2Q/1Q ratio (8.5 x 10(-3), plasma gave a very considerable 2Q/1Q ratio (2.3 x 10(-3). Because of its relatively high extracellular concentration, extracellular sodium may give a greater absolute 2Q signal than intracellular sodium in unmodified tissue samples. Based on these data, we conclude that a 2Q filter will not provide a useful measurement of intracellular sodium in in vivo tissue samples.     

Quantifying spatial and temporal variability of macroinvertebrate metrics

Since the introductions of the Habitat Directive and the European Water Framework Directive, water authorities are now obliged to monitor changes in conservation value/ecological quality on larger spatial scales (opposed to site scale), as well as to indicate the level of confidence and precision of the results provided by the monitoring programs in their river basin management plans (European Commission, 2000). To meet these requirements, analyses of the statistical power of the monitoring programs should be implemented. Currently, the statistical properties associated with aquatic monitoring programs are often unknown. We collected macroinvertebrate samples from 25 meso-eutrophic drainage ditches in the Netherlands and selected 7 taxonomic richness metrics for the evaluation of spatial and temporal variability. Simulations were performed to investigate the effects of changes in (1) the total number of species included in a taxonomic richness metric and (2) the relative number of rare species included in a taxonomic richness metric. Of the 7 metrics evaluated, the number of common species required the smallest number of monitoring sites, followed by the number of Gastropoda species, and the number of species. Also, results showed that metric variability will decrease when the proportion of rare species included in a taxonomic richness metric is reduced or the total number of species included is increased. Irrespective of the metric applied a large effort will be required to detect change within drainage ditches in the Wieden, due to high spatial variability. Therefore, we need to explore the possibilities of applying alternative more cost-effective methods for sampling and sample processing in biomonitoring programs.     

Reliability of using urinary and blood trichloroacetic acid as a biomarker of exposure to chlorinated drinking water disinfection byproducts

This study was designed to analyse the reliability of using urinary and blood trichloroacetic acid (TCAA) as a biomarker of exposure. A total of 46 healthy women consumed supplied TCAA-containing tap water for 15 days and provided urine and blood samples for TCAA measurements. The findings revealed that the reliability of measurements was excellent by using measures of TCAA ingestion, blood concentration and urinary excretion (intraclass correlation coefficients (ICC)?>?0.75, p??0.95, p?相似文献   

Laboratory measurement of urine albumin and urine total protein in screening for proteinuria in chronic kidney disease

Laboratory measurement of urine total protein has been important for the diagnosis and monitoring of renal disease for decades, and since the late 1990s, urine albumin has been measured to determine whether a diabetic patient has incipient nephropathy. Evolving understanding of chronic kidney disease (CKD) and, in particular, the cardiovascular risks that CKD confers, demands more sensitive detection of protein in urine. As well, evidence is now emerging that cardiovascular and all-cause mortality risks are increased at levels within the current 'normal' range for urine albumin. Standardisation is essential to permit valid application of universal decision points, and a National Kidney Disease Education Program/International Federation of Clinical Chemistry and Laboratory Medicine (NKDEP/IFCC) Working Party is making progress towards a reference system for urine albumin. In the meantime, available data suggest that Australasian laboratory performance is adequate in terms of precision and accuracy above current decision limits for urine albumin. In contrast, the complexity of proteins in urine makes standardisation of urine total protein measurement impossible. As well, urine total protein measurement is insufficiently sensitive to detect clinically important concentrations of urine albumin. An Australasian Expert Group, the Proteinuria Albuminuria Working Group (PAWG) has proposed that urine albumin/creatinine ratio is measured in a fresh, first morning, spot sample to screen for proteinuria in CKD. Both NKDEP/IFCC and PAWG emphasise the need for standardisation of sample collection and handling.