Characterization of Fluorescently Labeled Protein with Electrospray Ionization-MS and Fluorescence Spectroscopy: How Random is Random Labeling?

Solvent exposed lysine residues are abundantly present in many proteins. Their highly reactive ε-amino groups serve as universal targets for coupling with active esters of various extrinsic labels including a vast arsenal of fluorescent probes. Here, we describe fluorescent properties and preferential localization of two frequently used fluorescent labels, AlexaFluor488 (AF488) and Cy3, on the surface of a small highly soluble serum protein neutrophil gelatinase-associated lipocalin (NGAL), which serves as a diagnostic marker for acute kidney failure. Using a standard protocol for labeling with either AF488-SDP or AF488-NHS, we achieved >95% labeling efficiency of the protein as determined by UV-vis absorption and electrospray ionization (ESI)-MS. However, fluorescence intensity of the labeled protein was less than 10% of the expected value. To understand the unusually high quenching of the probe, we identified the sites of AF488 attachments by means of LC-MS/MS combined with trypsin digestion. Surprisingly, we found that the AF488 label is not randomly distributed among accessible lysines but predominantly bound to the residues K125, K126, or K135, which are located in the NGAL calyx and are likely quenched by neighboring tryptophans and tyrosines. In contrast, when NGAL was labeled with Cy3, the probe's fluorescence was almost fully retained. The LC-MS/MS data indicated that Cy3 was predominately bound to another lysine, K31, on the protein surface on the opposite side of the calyx. Our findings suggest that a combination of the inherent properties of the label and the specifics of the protein microenvironment may selectively lead probes to specific lysine residues and thus challenge the common view that protein labeling is a random process.

Cysteinylation of a monoclonal antibody leads to its inactivation.

Post-translational modifications can have a signification effect on antibody stability. A comprehensive approach is often required to best understand the underlying reasons the modification affects the antibody's potency or aggregation state. Monoclonal antibody 001 displayed significant variation in terms of potency, as defined by surface plasmon resonance testing (Biacore), from lot to lot independent of any observable aggregation or degradation, suggesting that a post-translational modification could be driving this variability. Analysis of different antibody lots using analytical hydrophobic interaction chromatography (HIC) uncovered multiple peaks of varying size. Electrospray ionization mass spectrometry (ESI-MS) indicated that the antibody contained a cysteinylation post-translational modification in complementarity-determining region (CDR) 3 of the antibody light chain. Fractionation of the antibody by HIC followed by ESI-MS and Biacore showed that the different peaks were antibody containing zero, one, or two cysteinylation modifications, and that the modification interferes with the ability of the modified antibody arm to bind antigen. Molecular modeling of the modified region shows that this oxidation of an unpaired cysteine in the antibody CDR would block a potential antigen binding pocket, suggesting an inhibition mechanism.

Epitope mapping and targeted quantitation of the cardiac biomarker troponin by SID-MRM mass spectrometry.

The absolute quantitation of the targeted protein using MS provides a promising method to evaluate/verify biomarkers used in clinical diagnostics. In this study, a cardiac biomarker, troponin I (TnI), was used as a model protein for method development. The epitope peptide of TnI was characterized by epitope excision followed with LC/MS/MS method and acted as the surrogate peptide for the targeted protein quantitation. The MRM-based MS assay using a stable internal standard that improved the selectivity, specificity, and sensitivity of the protein quantitation. Also, plasma albumin depletion and affinity enrichment of TnI by anti-TnI mAb-coated microparticles reduced the sample complexity, enhanced the dynamic range, and further improved the detecting sensitivity of the targeted protein in the biological matrix. Therefore, quantitation of TnI, a low abundant protein in human plasma, has demonstrated the applicability of the targeted protein quantitation strategy through its epitope peptide determined by epitope mapping method.

Introduction of the mass spread function for characterization of protein conjugates.

Traditionally, characterization of protein molecules conjugated with molecular probes is performed by UV-vis spectroscopy. This method determines the average incorporation ratio but does not yield information about the label distribution. Electrospray ionization mass spectroscopy (ESI-MS) allows direct measurement of the fraction of protein containing a given number of labels. However, for a glycosylated protein, this analysis can be severely limited due to spectral overlap of the labels and carbohydrates. To address this problem, we introduce the mass spread function (MSF) for conjugation analysis. By treating the ESI-MS spectrum of conjugated protein as the spectrum before conjugation convolved with the MSF, we are able to quantify the labeled protein population using a binomial distribution function. We first applied this procedure for characterization of labeled antibody F(ab')(2) fragments which do not contain carbohydrates. We then apply the MSF to fit spectra of entire conjugated monoclonal antibodies and quantify the distribution of labels in the presence of glycans.

Structural characterization of glycoprotein NGAL, an early predictive biomarker for acute kidney injury.

Neutrophil gelatinase-associated lipocalin (NGAL) is a promising new renal biomarker that can reduce the time to diagnose acute kidney injury (AKI). There is little information available about complex glycans on NGAL. Detailed structural characterization of NGAL is necessary to understand the structural variability of NGAL used as a standard in the NGAL immunoassay. This study demonstrated that 7-9% of mutant (C87S) recombinant NGAL was N-glycosylated and no O-glycosylation was detected. The NGAL sequence was confirmed by nanoLC/MS/MS following in gel and in solution trypsin digestion, and the N-glycosylation site was localized by MS/MS. Six different mutant recombinant NGAL samples (samples A-F) were analyzed in this study; however, these samples demonstrated two different glycan patterns. Forty-one N-glycans were detected in sample A and the more abundant N-glycans were unsialylated. Forty-three N-glycans were detected in sample F and the more abundant N-glycans were sialylated. Each of the other four samples (B-E) had a similar N-glycan pattern as sample F.

Development of an Abbott ARCHITECT cyclosporine immunoassay without metabolite cross-reactivity.

OBJECTIVE: We investigated the mechanism by which the ARCHITECT cyclosporine (CsA) chemiluminescent microparticle immunoassay (CMIA) eliminates cross-reactivity to CsA metabolites AM1 and AM9, despite its use of a monoclonal antibody which shows cross-reactivity in fluorescence polarization immunoassays. DESIGN AND METHODS: The CMIA was accomplished by incubating an extracted blood sample with magnetic microparticles coated with a very low amount of anti-CsA antibody. After a wash step the microparticles were incubated with a chemiluminescent CsA tracer, followed by a second wash step and measurement of chemiluminescence. The reagent concentrations of salt and detergent were optimized to maximize CsA binding and minimize metabolite interference. RESULTS: Elimination of CsA metabolite cross-reactivity was shown using purified metabolites and blood samples containing native CsA metabolites. The CMIA demonstrated precision and sensitivity acceptable for use in a clinical setting. CONCLUSION: We conclude that it is possible to eliminate CsA metabolite immuno-cross-reactivity by careful assay design.

Microheterogeneous monoclonal antibody subspecies with differential hepatitis C virus core antigen binding properties identified by SEC-HPLC.

A monoclonal antibody directed against the core protein of hepatitis C virus was characterized for its utility in a sandwich antigen immunoassay wherein the mAb was used as the conjugate. Analysis of unconjugated and acridinium-conjugated monoclonal IgG using a silica-based HPLC size exclusion column revealed the existence of a single, symmetrical peak. Subsequent analysis of unconjugated IgG using a methacrylate-based HPLC size exclusion column revealed the presence of two species of IgG, but only by using a low ionic strength mobile phase buffer. Independent conjugation and testing of the two species showed significant differential reactivity towards HCV core antigen. Isoelectric focusing gels indicated subtle differences in the subspecies composition. Measurement of target peptide dissociation constants using fluorescence correlation spectroscopy indicated that the two HPLC column fractions exhibited a two-fold difference in Kd in low salt buffer that disappeared in high salt buffer. ESI-MS analysis of the fractionated IgG peaks revealed a reduction sensitive modification of the IgG and F(ab')2 of approximately 674 Da. In addition, both IgG and F(ab')2 contained two major heavy chain subspecies differing by about 1216 Da that was reduction insensitive. These modifications were present in only the one of the two SEC-HPLC peaks. These results suggest that this monoclonal antibody consists of microheterogeneous subspecies that exhibit different antigen binding properties associated with differences in post-translational modification of the heavy chain variable region. The choice of size exclusion column matrix and buffer composition was critical to the identification of these monoclonal IgG subspecies.

State-of-the-art of serum testosterone measurement by isotope dilution-liquid chromatography-tandem mass spectrometry.

BACKGROUND: The recent interest of clinical laboratories in developing serum testosterone assays based on isotope dilution-liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) stems from the lack of accuracy of direct immunoassays. In this study, we assessed the accuracy and state of standardization (traceability) of 4 published ID-LC-MS/MS procedures in a method comparison with an ID-gas chromatography (GC)-MS reference measurement procedure listed in the database of the Joint Committee for Traceability in Laboratory Medicine. METHODS: The study used 58 specimens from different patient categories. Each specimen was measured in triplicate (ID-LC-MS/MS) and quadruplicate (ID-GC-MS) in independent runs. RESULTS: The testosterone concentrations by ID-GC-MS were 0.2-4.4 nmol/L (women), 0.2-2.0 nmol/L (hypogonadal man), and 10.1-31.3 nmol/L (normogonadal men). For ID-GC-MS, the CV was nearly constant, with a median of 1.0%; for ID-LC-MS/MS, it was concentration-dependent, with a median of up to 8%. Weighted Deming regression gave mean slopes, intercepts, and correlation coefficients of 0.90-1.11, -0.055-0.013 nmol/L, and 0.993-0.997, respectively. The % difference plot showed between 7% and 26% of the results outside a total error limit of 14%, with median deviations from ID-GC-MS between -9.6 and 0.4%. CONCLUSIONS: This study demonstrated fairly good accuracy and standardization of the tested ID-LC-MS/MS procedures. Performance differences between procedures were evident in some instances, due to improper calibration and between-run calibration control. This emphasizes the need for thorough validation, including traceability, of new ID-LC-MS/MS procedures.

Mass spectrometric and physiological validation of a sensitive, automated, direct immunoassay for serum estradiol using the Architect.

BACKGROUND: Measurement of estradiol (E(2)) plays a critical role in the diagnosis and clinical management of reproductive disorders. The challenge for all currently available direct methods for measuring E(2) is to provide accuracy and precision across a wide dynamic range. METHODS: We describe the development and multi-site performance evaluation of a direct E(2) assay on the Architect i2000. Assay performance and method comparisons were performed by testing specimens from men, healthy women with regular menstrual cycles, and post-menopausal women using the Architect assay and isotope dilution, gas chromatography-mass spectrometry (ID/GC-MS). Reference intervals were established by testing prospectively collected daily blood draws from 42 healthy women, 72 postmenopausal women and 101 males. RESULTS: No unexpected cross-reactivity or interference was observed for over 40 compounds tested. Recovery was 100+/-10% in the presence of estrone and estriol. Functional sensitivity (%CV<20%) was <15 pg/ml.(1) The imprecision of the assay was <7.1% (total CV), <2.5%, and <2.3% for control sera containing 45, 190, and 600 pg/ml estradiol, respectively. The assay had a correlation of y=1.033 x+0.3156, r(2)=0.99, n=131 compared to ID/GC-MS. Reference intervals for the current Architect Estradiol assay are reported. CONCLUSIONS: Format changes resulted in dramatic improvement in the performance and accuracy of this direct, fully automated assay. The assay is standardized by ID/GC-MS. The assay is clinically useful for serum concentrations from 15 to >4000 pg/ml.

Performance characteristics of eight estradiol immunoassays.

Measurement of estradiol is useful in assisted reproduction, evaluation of infertility, menopause, and male feminization. The analytic performance of 8 estradiol immunoassays was evaluated. The imprecision and accuracy of the Access, ADVIA Centaur, ARCHITECT i2000, AutoDELFIA, Elecsys 2010, IMMULITE 2000, and Vitros ECi estradiol assays (see text for proprietary information) were evaluated by using an isotope dilution-gas chromatography-mass spectrometry (ID-GC-MS) reference method. The coefficient of variation (CV) ranged from 6.9% on the Elecsys 2010 to 42.6% on the ADVIA Centaur at an estradiol concentration of 18 pg/mL (66 pmol/L), with the ARCHITECT i2000 assay in development and the Vitros ECi having a CV below 10% at this estradiol concentration. Agreement between the automated assays and ID-GC-MS was variable, with slopes ranging from 0.87 to 1.20. The Access, ARCHITECT i2000 in development, and the IMMULITE 2000 were the most accurate, with slopes of 0.99, 0.98, and 1.03, respectively. These findings indicate that the ARCHITECT i2000 estradiol assay in development had the best precision and accuracy of the assays evaluated for measurement of serum estradiol concentrations.