Quantification of matrix metalloprotease-9 in bronchoalveolar lavage fluid by selected reaction monitoring with microfluidics nano-liquid-chromatography–mass spectrometry

Microtrap-assisted microfluidic magnetic separation and concentration for ultrasensitive immunoassays of biomarkers

Precise and accurate quantitation of important biomarkers is significant, especially in early-stage diseases diagnosis. To realized effective biosample preparation and trace-level biomarker detection, a microtrap-assisted microfluidic magnetic immunoassays (μMI) method was developed in this work. A microtrap was fabricated inside the straight microchannel of μMI device to help magnetic separation and concentration of immunocomplexes. These immunocomplexes were enriched in microtrap of μMI device to accomplish selective and sensitive biomarker detection. Horseradish peroxidase-labeled magnetic beads were employed to evaluate assay feasibility and microtrap effect on assay sensitivity. The microtrap-assisted μMI was then applied for model biomarkers detection. The limits of detection of μMI were 0.025 pg/mL for monocyte chemoattractant protein-1 (MCP-1) and 0.021 pg/mL for matrix metalloproteinase-9 (MMP-9), which corresponded up to 2014-fold sensitivity improvement compared to their standard microwell enzyme-linked immunosorbent assay (ELISA) results. In addition, the selectivity and reproducibility of microtrap-assisted μMI were confirmed. In clinical serum sample analysis, recoveries of 91.3%-106.7% with relative standard deviations less than 6.1% were obtained for MCP-1 and MMP-9, and method accuracy was verified by commercial ELISA kit. The developed μMI can accomplish ultratrace biomarker detection offering practical tool for laboratorial and clinical research.

An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples

BACKGROUND

Clinical bronchoalveolar lavage fluid (BALF) samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease. However, mass spectrometry (MS)-based proteomic analysis of BALF is challenged by the dynamic range of protein abundance, and potential for interfering contaminants. A robust, MS-based proteomics compatible sample preparation workflow for BALF samples, including those of small and large volume, would be useful for many researchers.

RESULTS

We have developed a workflow that combines high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, that is compatible with either qualitative or quantitative MS-based proteomic analysis. The workflow includes a value-added collection of endogenous peptides for peptidomic analysis of BALF samples, if desired, as well as amenability to offline semi-preparative or microscale fractionation of complex peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis. We demonstrate the effectiveness of this workflow on BALF samples collected from COPD patients, including for smaller sample volumes of 1-5 mL that are commonly available from the clinic. We also demonstrate the repeatability of the workflow as an indicator of its utility for quantitative proteomic studies.

CONCLUSIONS

Overall, our described workflow consistently provided high quality proteins and tryptic peptides for MS analysis. It should enable researchers to apply MS-based proteomics to a wide-variety of studies focused on BALF clinical specimens.

Biosensors and bioassays for determination of matrix metalloproteinases: state of the art and recent advances

Matrix metalloproteinases (MMPs) are closely associated with various physiological and pathological processes, and have been regarded as potential biomarkers for severe diseases including cancer. Accurate determination of MMPs would advance our understanding of their roles in disease progression, and is of great significance for disease diagnosis, treatment and prognosis. In this review, we present a comprehensive overview of the developed bioassays/biosensors for detection of MMPs, and highlight the recent advancement in nanomaterial-based immunoassays for MMP abundance measurements and nanomaterial-based biosensors for MMP activity determination. Enzyme-linked immunosorbent assay (ELISA)-based immunoassays provide information about total levels of MMPs with high specificity and sensitivity, while target-based biosensors measure the amounts of active MMPs, and allow imaging of MMP activities in vivo. For multiplex and high-throughput analysis of MMPs, microfluidics and microarray-based assays are described. Additionally, we put forward the existing challenges and future prospects from our perspective.

HPLC-MS/MS method optimisation for matrix metalloproteinase 3 and matrix metalloproteinase 9 determination in human blood serum using target analysis

A quantitative analysis of zinc endopeptidases matrix metalloproteinase 9 (MMP9) and matrix metalloproteinase 3 (MMP3) from human blood serum are presented. Both matrix metalloproteinases (MMP) are present in human blood serum and can be used as biomarkers for different diseases. The analysis was performed using LC-MS/MS with a triple quadrupole mass spectrometer, based on two specific peptides of each MMP in comparison with an enzyme-linked immunosorbent assay (ELISA). While the conditions for the LC-MS/MS analysis of MMP9 peptides were previously reported for bronchoalveolar lavage fluid, the analysis of MMP3 peptides was newly quantified for human blood serum herein for the first time. For MMP3, the linear behaviour was determined in the concentration range from 1.0-200.0ng/mL (R²=0.997) with an LLOD of 0.5ng/mL. For MMP9, linearity was determined in the concentration range from 6.5-65.0ng/mL (R²=0.995) with an LLOD of 2.0ng/mL.

Development of a label-free SPR sensor for detection of matrixmetalloproteinase-9 by antibody immobilization on carboxymethyldextran chip

Surface plasmon resonance (SPR) immunosensor has been widely utilized for monitoring antigen-antibody interactions. The sensor measures changes of refractive index upon binding of analyte molecules to specific ligand immobilized on the sensor chip. This effort reports development of SPR immunosensor for real-time and label-free detection of recombinant human matrix metalloproteinases-9 (MMP-9), which has been associated with malignant tumor progression and metastasis by matrix degradation. MMP-9 was expressed in Escherichia coli BL21 and purified by Ni-NTA agarose column. CMD 50 D was activated by EDC/NHS for immobilization of monoclonal anti-MMP-9. Atomic force microscopy images showed uniform distribution of anti-MMP-9 over the sensor chip. Equilibrium constant (KD), maximum binding capacity (Rmax) and ∆Gb values for interaction of MMP-9 and anti-MMP-9 were 0.4nM, 680 µRIU and -53.51kJ/mol, respectively. Concentration of MMP-9 in saliva samples was determined, with linearity in the range of 10-200ng/mL. The limit of detection was found to be 8pg/mL, being lower than most of the previously reported techniques.

Recent applications of CE- and HPLC-MS in the analysis of human fluids

The present review intends to cover the literature on the use of CE-/LC-MS for the analysis of human fluids, from 2010 until present. It has been planned to provide an overview of the most recent practical applications of these techniques to less extensively used human body fluids, including, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate, tear fluid, breast fluid, amniotic fluid, and cerumen. Potential pitfalls related to fluid collection and sample preparation, with particular attention to sample clean-up procedures, and methods of analysis, from the research laboratory to a clinical setting will also be addressed. While being apparent that proteomics/metabolomics represent the most prominent approaches for global identification/quantification of putative biomarkers for a variety of human diseases, evidence is also provided of the suitability of these sophisticated techniques for the detection of heterogeneous components carried by these fluids.

Monitoring the biomolecular interactions and the activity of Zn-containing enzymes involved in conformational diseases: experimental methods for therapeutic purposes

Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates/inhibitors and how environmental factors can affect enzyme activities. In this scenario, nuclear magnetic resonance, X-ray diffraction, mass spectrometric (MS), and optical methods occupy a very important role in elucidating different aspects of the ZnMPs-substrates/inhibitors interaction, ranging from identification of cleavage sites to quantitation of kinetic parameters and inhibition constants. Here, an overview of all the main achievements in the application of different experimental approaches with special attention to MS methods to the investigation of ZnMPs-substrates/inhibitors interaction is given. A general MS experimental protocol which has been proved to be useful to study such interactions is also described.

Lab-on-a-Chip hyphenation with mass spectrometry: strategies for bioanalytical applications

The Lab-on-a-Chip concept aims at miniaturizing laboratory processes to enable automation and/or parallelization via microfluidic chips that are capable of handling minute sample volumes. Mass spectrometry is nowadays the detection method of choice, because of its selectivity, sensitivity and wide application range. We review the most interesting examples over the last two-and-a-half years where the two techniques were used for bioanalytical applications. Furthermore, we discuss the merits and limitations of such hyphenated systems. We inventorize the reported applications and approaches. We see an ongoing trend towards chip-based liquid chromatography-mass spectrometry usage and small volume analysis applications, particularly in the field of proteomics where bottom-up approaches profit from chip-based technologies and hyphenation with complex cell cultures.

Applications of low-flow LC–SRM for the analysis of large molecules in pharmaceutical R&D

Although ligand-binding assays are frequently employed to measure large molecules, the use of LC–SRM assays is increasingly popular due to the inherent selectivity advantage and the ability to operate without exquisitely selective antibodies. Until recently LC–SRM assays have been unable to compete with ligand-binding assays in terms of sensitivity. However, the use of low-flow chromatography prior to mass spectrometry has played a crucial role in increasing the sensitivity of LC–SRM platforms and enabling measurements of large molecules that had previously been unmeasurable. In this article, we highlight some technical advances, describe strategies for employing low-flow chromatography, and review recent literature that describes implementation of low-flow LC–SRM to support large-molecule analysis in pharmaceutical R&D.

Detection of endogenous matrix metalloprotease-12 active form with a novel broad spectrum activity-based probe

Matrix metalloproteases (MMPs) have attracted considerable attention as critical mediators of pathological tissue remodeling processes. However it remains an unresolved challenge to detect their active forms in biological samples. To prove the efficacy of a recently developed MMP activity-based probe, we examined the content in MMP active forms of bronchoalveolar lavage fluids (BALf) from male C57BL/6 mice exposed to ultrafine carbon black nanoparticles, a model of chronic obstructive pulmonary disease. This probe was shown to label proteins, mostly expressed in BALf of mice exposed to nanoparticles. Using competition assays with a selective MMP-12 inhibitor as well as MMP-12 knock-out mice, one of these proteins was identified as the active form of the catalytic domain of MMP-12. This new probe can detect the active form of MMP-12 down to a threshold of 1 fmol. Radioactive counting showed the concentration of the active form of MMP-12 to be around 1 fmol/μl in BALf from nanoparticle-treated mice. A less sensitive probe would therefore not have detected MMP-12. As the probe can detect other MMPs in the femtomolar range, it is a potentially powerful tool for monitoring the levels of MMP active forms in various diseases.

Nano-scale liquid chromatography/mass spectrometry and on-the-fly orthogonal array optimization for quantification of therapeutic monoclonal antibodies and the application in preclinical analysis

Therapeutic monoclonal antibodies (mAbs) constitute a group of highly effective agents for treating various refractory diseases. Nonetheless it is challenging to achieve selective and accurate quantification of mAb in pharmaceutical matrices, which is required by PK studies. Liquid chromatography/mass spectrometry under selected reaction monitoring mode (LC/SRM-MS) is emerging as an attractive alternative to immunoassays because of the high specificity and multiplexing capacity it provides, but may fall short in terms of sensitivity, reliability and quantitative accuracy. Moreover, the strategy for optimization of the MS conditions for many candidates of signature peptides (SP) and the selection of the optimal SP for quantification remains elusive. In this study, we employed a suite of technical advances to overcome these difficulties, which include: (i) a nano-LC/SRM-MS approach to achieve high analytical sensitivity, (ii) a high-resolution nano-LC/LTQ/Orbitrap for confident identification of candidate peptides, (iii) an on-the-fly orthogonal array optimization (OAO) method for the high-throughput, accurate and reproducible optimization for numerous candidate peptides in a single LC/MS run without using synthesized peptides, (iv) a comprehensive evaluation of stability of candidates in matrix using the optimized SRM parameters, (v) the use of two unique SP for quantification of one mAb to gauge possible degradation/modification in biological system and thus enhancing data reliability (e.g. rejection of data if the deviation between the two SP is greater than 25%) and (vi) the utilization of purified target protein as the calibrator to eliminate the risk of severe negative biases that could occur when a synthesized peptide is used as calibrator. To show a proof of concept, this strategy is applied in the quantification of cT84.66, a chimeric, anti-CEA antibody, in preclinical mouse models. A low detection limit of the mAb down to 3.2 ng/mL was achieved, which is substantially more sensitive than established immunoassay methods for anti-CEA antibodies. The quantitative method showed good linearity (within the range of 12.9 ng/mL to 32.3 μg/mL in plasma), accuracy and precision. Additionally, the ultra-low sample consumption (2 μL plasma per preparation) permits the acquisition of an entire set of time course data from the same mouse, which represents a prominent advantage for PK study using small-animal models. The developed method enabled an accurate PK investigation of cT84.66 in mice following intravenous and subcutaneous administrations at relatively low doses over an extended period of time. The strategy employed in this study can be easily adapted to the sensitive and accurate analysis of other mAb and therapeutic proteins.