An accurate method for the quantitation of Fmoc-derivatized solid phase supports

By performing the Fmoc resin loading determination with DBU instead of piperidine, highly reproducible results were obtained that showed excellent correlation with data obtained by independent analytical methods.     

An efficient quantitation method of next-generation sequencing libraries by using MiSeq sequencer

Library quantitation is a critical step to obtain high data output in Illumina HiSeq sequencers. Here, we introduce a library quantitation method that uses the Illumina MiSeq sequencer designated as quantitative MiSeq (qMiSeq). In this procedure, 96 dual-index libraries, including control samples, are denatured, pooled in equal volume, and sequenced by MiSeq. We found that relative concentration of each library can be determined based on the observed index ratio and can be used to determine HiSeq run condition for each library. Thus, qMiSeq provides an efficient way to quantitate a large number of libraries at a time.     

An improved method for the covalent attachment of glycolipids to solid supports and macromolecules.

A simplified method is presented for the oxidation of the olefinic bond of the sphingosine moiety of glycosphingolipids to a carboxyl group. Coupling of such "glycolipid acids" to glass beads, agarose gels, proteins, and polyacrylic hydrazide polymers is described. Solid supports and macromolecules that have been derivatized in this fashion are useful reagents for a variety of studies in cell biology and immunology.     

Strategies for quantitation of phosphoproteomic data

Recent developments in phosphoproteomic sample-preparation techniques and sensitive mass spectrometry instrumentation have led to large-scale identifications of phosphoproteins and phosphorylation sites from highly complex samples. This has facilitated the implementation of different quantitation strategies in order to study the biological role of protein phosphorylation during disease progression, differentiation or during external stimulation of a cellular system. In this article, a brief summary of the most popular strategies for phosphoproteomic studies is given; however, the main focus will be on different quantitation strategies. Methods for metabolic labeling, chemical modification and label-free quantitation and their applicability or inapplicability in phosphoproteomic studies are discussed.     

Stable isotope labeling method targeting terminal tyrosine for relative peptide quantitation using mass spectrometry

Many neuropeptides lack suitable amino acid residues for modification by existing selective isotope labeling methods and use in relative quantitation by mass spectrometry. To address this issue, a new stable isotope labeling method that targets tyrosine residues by coupling with light cysteine (d₀) or heavy cysteine (d₂) in the presence of tyrosinase was developed. Optimal derivatization conditions for 1 μM leucine-enkephalin were achieved when 10 mM cysteine and 200 U/ml tyrosinase at pH 6.8 to 7.2 were used for a 60-min incubation period at room temperature. Under these conditions, leucine-enkephalin present at concentrations as low as 125 nM was successfully labeled. When comparisons between the lightly labeled (d₀) and heavily labeled (d₂) forms were made, a discrepancy between the actual concentration ratio and the raw peak intensity ratio was observed; this is due to the overlap of an isotopic peak of the d₀ with the monoisotopic peak of d₂. Fortunately, this discrepancy can be corrected by one of two simple computational approaches described. The quantitative labeling of this method to neuropeptides with the terminal tyrosine was confirmed and provides an alternative when other selective isotope-coded affinity tagging methods are not suitable.     

Heparin requirement for the quantitation of fibrinogen production by primary hepatocyte cultures

We have reported a rapid method for the quantitation of proteins secreted in culture media ([12.]). Using the same method, we observe that serum-free rat hepatocyte cultures exhibited a 100% increase in detectable secreted fibrinogen-antigen in the presence of 1 unit/ml heparin or greater at 24 h of culture. The amount of transferrin, haptoglobin, and albumin detected was unaltered by the presence of heparin. Since heparin is known to affect certain cellular functions, the fates of [³⁵S]methonine-labeled fibrinogen in cell extracts and culture media were examined employing pulse-chase experiments. Labeled intracellular fibrinogen disappeared at similar rates and was initially released into the media in similar amounts in the presence or absence of heparin. At 8 h during the chase, there was a 40–50% reduction in fibrinogen-antigen in spent culture medium lacking heparin. The presence of heparin did not alter the proteolytic degradation of secreted fibrinogen as determined by immunoblotting of spent culture media proteins separated by polyacrylamide gel electrophoresis. In vitro experiments indicate that clotting of fibrinogen by thrombin reduces the amount of immunodetectable fibrinogen. The results indicate that heparin increases the amount of detectable fibrinogen secreted by cultured hepatocytes by preventing clotting and not by stimulating synthesis or secretion or by inhibiting degradation. Hence, it is critically important to include heparin when secreted fibrinogen is quantitated by the method that we have developed.     

An immunoaffinity liquid chromatography-tandem mass spectrometry assay for the quantitation of matrix metalloproteinase 9 in mouse serum

An immunoaffinity liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the quantitation of the zinc endopeptidase matrix metalloproteinase 9 (MMP-9) from mouse serum. Sample preparation for the assay included magnetic bead-based enrichment using an MMP-9 antibody and was performed in a 96-well plate format using a liquid-handling robotic platform. The surrogate peptide GSPLQGPFLTAR derived from MMP-9 by trypsin digestion was monitored using an on-line capillary flow trap-release chromatography setup incorporating a series of trap columns (C18, strong cation exchange, and another C18) prior to nanoflow chromatography and nanospray ionization with selected reaction monitoring (SRM) detection. The assay was fit-for-purpose validated and found to be accurate (<15% interbatch relative error) and precise (<15% interbatch coefficient of variation) across a range from 0.03 to 7.3 nM mouse MMP-9. Finally, the method was employed to measure MMP-9 concentrations in 30 naïve mouse serum samples, and results were compared with those obtained by an immunoassay.     

An accurate method for measurement of aldosterone production

A method is described for isolation of the acid-hydrolysable metabolite of aldosterone in sufficient purity to measure accurately the daily production rate. Values obtained with six hospital patients were 84-131mug./day on a daily intake of 100m-equiv. of Na(+) and 227-464mug./day on a daily intake of 10m-equiv. of Na(+). Corresponding values for aldosterone excretion were also recorded, but these are a poor index of production rate since they represent from 1.6 to 9.8% of the total daily output of aldosterone.     

An easy and accurate agarose gel assay for quantitation of bacterial plasmid copy numbers

An assay for quantitation of plasmid copy numbers in bacterial cell cultures has been developed and validated. The method combines isolation of total bacterial DNA (including both plasmid and genomic DNA), running a series of twofold dilutions of total DNA in an agarose gel followed by ethidium bromide staining, and subsequent scanning of the gel picture negatives. We have developed a novel set of rules for integration of the scan data that allows us to achieve high assay precision, accuracy, and sensitivity. The assay validation results were as follows: intra- and interassay precision with %CV of 8.2-9.9 and 7.1-9.8%, respectively; ruggedness with %CV of 9.3-17.5%; spike recovery of 80-102%; and sensitivity of 1 plasmid copy per genome.     

An improved method for the selective detection of fungi in hospital waters by solid phase cytometry

Yeast cells and mould spores can be fluorescently labelled with the viability stain carboxyfluorescein diacetate (CFDA) and detected on a membrane filter by laser scanning (solid phase cytometry, SPC). Although the selectivity of an existing commercial SPC procedure for fungi is ensured by using a 2 microm pore size membrane filter and a pre-incubation on a proprietary spore swelling/activation medium, some bacteria are still co-detected. In the present study, the selectivity for fungi has been enhanced by combining the green fluorescent CFDA with a second red fluorescent label, i.e. TRITC-concanavalin A, targetting fungal but not commonly bacterial cells. Additional improvements resulted from the prolongation of the pre-incubation and from the extra-rinsing of the membrane filter. The improved method was applied to detect fungi in hospital waters, dialysis fluids and endoscopic rinse waters. In general, SPC detected more fungi in water than plate methods. The occurrence of fungi in dialysis fluid and endoscopic rinse water was rare. Evidence for the presence of fungal viable but non-culturable (VBNC) cells in water was weak.     

Hybridization of biotinylated oligo(dT) for Eukaryotic mRNA quantitation

Quantitation of mRNA content in samples of total cellular RNA is required for the analysis of Northern blot hybridization to estimate the relative level of specific gene expression. Commonly used methods based on UV absorbance and dye staining measure only total RNA, and mRNA normalization by probing for mRNA levels of housekeeping genes, such as β-actin and glyceraldehyde-3-phosphate dehydrogenase, assumes a constant level of their expression, which, in fact, may vary as a function of cell proliferation and differentiation. We describe here a nonradioactive, slot-blotting method for quantifying eukaryotic mRNA levels using a biotinylated oligo(dT) probe, which hybridizes directly to the 3′-polyadenylated sequence of eukaryotic mRNAs. The method provides a more accurate estimation of mRNA content in total RNA samples and should be applicable for quantitative Northern analysis.     

Targeted quantitation of CVD-linked plasma proteins for biomarker verification and validation

Despite significant advances in treatment, cardiovascular disease (CVD) remains one of the leading causes of morbidity and mortality in developed and developing countries. Judicious monitoring of common risk factors has been unable to control this global epidemic, necessitating novel biomarkers for improved screening and earlier disease detection and management. Although numerous plasma proteins have been associated with CVD, only a few of these potential biomarkers have been validated for clinical use. Here we review the quantitative proteomic methods used to verify and validate new biomarker candidates in human plasma. These methods center on a bottom-up approach involving multiple or selected reaction monitoring, for targeted detection, with stable isotope-labeled standards, for peptide normalization. Also included are a discussion of future strategies for improved CVD protein biomarker verification and validation, recommendations for method translation to the clinic, and future projections for protein biomarker research.     

Thin-layer chromatography — flame ionization detection and the quantitation of marine neutral lipids and phospholipids

A method is described whereby a complete analysis of individual neutral lipid and phospholipid classes in marine animal total lipid can be achieved using an latroscan TLC-FID analyser. The method involves separate analyses of two samples of total lipid in solvents designed to separate neutral and polar lipid classes, together with calibration by a composite standard similar in composition to the sample under analysis. The method does not depend on the degree of unsaturation of the fatty acids present, is rapid and compares well in accuracy with conventional combined gravimetric, colouritnetric, and densitometric procedures.     

Fluoroprofile, a fluorescence-based assay for rapid and sensitive quantitation of proteins in solution

The development of a sensitive fluorescence-based assay for the quantitative determination of protein concentration is described. The assay is based on the natural product epicocconone, which produces a large increase in fluorescence quantum yield upon binding to detergent-coated proteins in solution. There is a concomitant shift in the emission maximum from 520 to 605 nm after binding, which results in low background signal allowing a linear dynamic range of 40 ng/mL to 200 microg/mL for most proteins. There is little protein-to-protein variation except for iron-containing proteins and the assay can be used so that it is tolerant of chemicals commonly used in 2-D sample buffers. The assay is more sensitive than standard absorption assays such as the Bradford and Lowry assays, and has a greater dynamic range and sensitivity than other fluorescent assays.     

An ultramicro method for quantitation of amino acids in biological fluids

A modification of the commercially available SZ-14 reorienting density gradient rotor is described whereby continuous sample flow with density gradient isopycnic banding may be utilized. This permits the fractionation of large volumes of dilute homogenates with excellent recovery and purity. The technique is demonstrated for the isolation of nuclei and particles of mitochondrial size.     

Reagents for the selective immobilization of oligonucleotides on solid supports

New reagents (CPGs and phosphoramidites) for automatic solid phase synthesis of modified oligonucleotides were designed. Three oligonucleotides carrying fluorescent label at the 5'-terminus and an anchor group at the 3'-terminus were prepared and their immobilization in orthogonal conditions on solid supports was studied.     

Convenient solid phase synthesis method for the preparation of cysteine C-terminally derivatized peptides

Summary This paper describes a novel solid phase peptide synthesis method for the systematic C-terminal modification of cysteine-containing peptides. In this method, cysteine is linked to chloromethylated polystyrene resin by its thiol functionality, followed by protection of the N-terminus and derivatization of the carboxylic acid to esters or amides. We report here on examples of the methodology and its application to the synthesis of Ac-Asp-cyclo(Cys-Gly-Pro-Cys)-NHBzl, a cyclic peptide amide. The method has been applied to the synthesis of complex esters as well as amides.Abbreviations Ac acetyl - AcN acetonitrile - Ac₂O acetic anhydride - AcOH acetic acid - Boc t-butyloxycarbonyl - BOP benzotriazol-1-yl-oxy-tris-(dimethylamino)-phosphonium hexafluorophosphate - Bzl benzyl - cHex cyclohexyl - DBU 1,8-diazabicyclo[5.4.0]-undec-7-ene - DCC N,N-dicyclohexylcarbodiimide - DCM dichloromethane - DIEA diisopropylethylamine - DMF dimethylformamide - DMS dimethylsulfide - HOB 1-hydroxybenzotriazole - MBzl 4-methyl benzyl - MeOH methanol - TEA triethylamine - TEAP triethylammonium phosphate - TFA trifluoroacetic acid