Origins, Technological Advancement, and Applications of Peptidomics

Peptidomics is the comprehensive characterization of peptides from biological sources instead of heading for a few single peptides in former peptide research. Mass spectrometry allows to detect a multitude of peptides in complex mixtures and thus enables new strategies leading to peptidomics. The term was established in the year 2001, and up to now, this new field has grown to over 3000 publications. Analytical techniques originally developed for fast and comprehensive analysis of peptides in proteomics were specifically adjusted for peptidomics. Although it is thus closely linked to proteomics, there are fundamental differences with conventional bottom-up proteomics. Fundamental technological advancements of peptidomics since have occurred in mass spectrometry and data processing, including quantification, and more slightly in separation technology. Different strategies and diverse sources of peptidomes are mentioned by numerous applications, such as discovery of neuropeptides and other bioactive peptides, including the use of biochemical assays. Furthermore, food and plant peptidomics are introduced similarly. Additionally, applications with a clinical focus are included, comprising biomarker discovery as well as immunopeptidomics. This overview extensively reviews recent methods, strategies, and applications including links to all other chapters of this book.

Quantification of Amyloid-β in Plasma by Simple and Highly Sensitive Immunoaffinity Enrichment and LC-MS/MS Assay

Background

Numerous immunoassays have been developed to quantify amyloid β1-40 (Aβ40) and amyloid β1-42 (Aβ42). Nevertheless, given the low concentration of Aβ and the high levels of interfering factors in plasma, quantification of plasma Aβ is still challenging. To overcome the problems related to the specificity of Aβ immunoassays, this study aimed to develop an immunoaffinity enrichment and LC-MS/MS (IA-MS) assay.

Methods

We developed an IA-MS assay using antibody-labeled magnetic beads for purification and LC-MS/MS for Aβ quantification. To avoid the loss of Aβ due to aggregation in acidic buffer, we used alkaline elution buffer for immunoaffinity enrichment. The concentrations of the Aβs in plasma samples were measured, and the correlation between the plasma and cerebrospinal fluid (CSF) Aβ42/Aβ40 ratio was also evaluated.

Results

The intensities of the Aβ mass peaks were significantly higher with the alkaline elution buffer than with the acidic elution buffer (Aβ40: 3.6-fold, Aβ42: 5.4-fold). This assay exhibited high reproducibility (intra-assay and inter-assay precision, %CV <15), and the working ranges of Aβ40 and Aβ42 were determined to be 21.7 to 692.8 pg/mL and 5.6 to 180.6 pg/mL, respectively. The concentrations of Aβ40 and Aβ42 in plasma were measured by IA-MS, and the plasma Aβ42/Aβ40 ratio was correlated with the CSF Aβ42/Aβ40 ratio (rs = 0.439, P < 0.01).

Conclusions

The IA-MS assay has sufficient analytic performance for measuring endogenous Aβ40 and Aβ42 in plasma. This assay can lead to new lines of clinical discovery related to amyloid pathology.

Linking (Pyr)1apelin-13 pharmacokinetics to efficacy: Stabilization and measurement of a high clearance peptide in rodents

Apelin, the endogenous ligand for the APJ receptor, has generated interest due to its beneficial effects on the cardiovascular system. Synthesized as a 77 amino acid preproprotein, apelin is post-translationally cleaved to a series of shorter peptides. Though (Pyr)¹apelin-13 represents the major circulating form in plasma, it is highly susceptible to proteolytic degradation and has an extremely short half-life, making it challenging to quantify. Literature reports of apelin levels in rodents have historically been determined with commercial ELISA kits which suffer from a lack of selectivity, recognizing a range of active and inactive isoforms of apelin peptide. (Pyr)¹apelin-13 has demonstrated beneficial hemodynamic effects in humans, and we wished to evaluate if similar effects could be measured in pre-clinical models. Despite development of a highly selective LC/MS/MS method, in rodent studies where (Pyr)¹apelin-13 was administered exogenously the peptide was not detectable until a detailed stabilization protocol was implemented during blood collection. Further, the inherent high clearance of (Pyr)¹apelin-13 required an extended release delivery system to enable chronic dosing. The ability to deliver sustained doses and stabilize (Pyr)¹apelin-13 in plasma allowed us to demonstrate for the first time the link between systemic concentration of apelin and its pharmacological effects in animal models.

Development and validation of an IA-LC/MS method to quantitate active and total B-type natriuretic peptide in human plasma

Aim: Patients with elevated levels of B-type natriuretic peptide (BNP) and/or NT-proBNP as measured by clinical tests have an elevated risk of heart failure (HF). Despite utility in large clinical studies, both assays are plagued by large biological variability and specificity issues. To address these concerns and further investigate BNP in the HF setting, we developed an LC/MS assay to characterize the ratio of active to total BNP. Results: We have developed and validated a novel immunoaffinity LC/MS assay to measure BNP-derived fragments, as well as ‘total BNP’ in human plasma. The ratio of active BNP1–32 to total BNP in 11 HF subjects was found to be <8%, and the sum of detectable BNP fragments contributed approximately 20% of total BNP. Conclusion: We developed an assay with the specificity to measure the active form of BNP, which may aid in the accurate diagnosis and better management of HF.

[Pyr1]-Apelin-13 delivery via nano-liposomal encapsulation attenuates pressure overload-induced cardiac dysfunction

Nanoparticle-mediated sustained delivery of therapeutics is one of the highly effective and increasingly utilized applications of nanomedicine. Here, we report the development and application of a drug delivery system consisting of polyethylene glycol (PEG)-conjugated liposomal nanoparticles as an efficient in vivo delivery approach for [Pyr1]-apelin-13 polypeptide. Apelin is an adipokine that regulates a variety of biological functions including cardiac hypertrophy and hypertrophy-induced heart failure. The clinical use of apelin has been greatly impaired by its remarkably short half-life in circulation. Here, we investigate whether [Pyr1]-apelin-13 encapsulation in liposome nanocarriers, conjugated with PEG polymer on their surface, can prolong apelin stability in the blood stream and potentiate apelin beneficial effects in cardiac function. Atomic force microscopy and dynamic light scattering were used to assess the structure and size distribution of drug-laden nanoparticles. [Pyr1]-apelin-13 encapsulation in PEGylated liposomal nanocarriers resulted in sustained and extended drug release both in vitro and in vivo. Moreover, intraperitoneal injection of [Pyr1]-apelin-13 nanocarriers in a mouse model of pressure-overload induced heart failure demonstrated a sustainable long-term effect of [Pyr1]-apelin-13 in preventing cardiac dysfunction. We concluded that this engineered nanocarrier system can serve as a delivery platform for treating heart injuries through sustained bioavailability of cardioprotective therapeutics.

Assessment of the metabolism of therapeutic proteins and antibodies

INTRODUCTION

In the last decade, our increased knowledge of factors governing the pharmacokinetics and metabolism of biologics (recombinant therapeutic proteins) has driven, and will continue to support, biological engineering and the design of delivery systems for more efficient biologics. Further research in analytical methods for assessing their in vitro and/or in vivo metabolism will also support these developments.

AREAS COVERED

In this review we will discuss the main components affecting the metabolism of biologics, and try to demonstrate how novel analytical evaluations will facilitate their future development. We will focus on the use of radiolabeled drugs, ligand-binding assays and mass spectrometry.

EXPERT OPINION

Future marketed biologics will be complex structures, such as glycoengineered, fused, or chemically modified proteins. Their in vivo efficiencies will be strongly dependent on their metabolic stabilities. Similarly to small molecular drugs, for which in vitro and in vivo biochemical platforms and analytical techniques have helped to rationalize preclinical and clinical developments, we would expect this also to translate to effective approaches to study the metabolism of biologics in the near future. Mass spectrometry should emerge as a standard technique for in vivo characterization of the biotransformation products of biologics.

Quantification of Tau in Cerebrospinal Fluid by Immunoaffinity Enrichment and Tandem Mass Spectrometry

BACKGROUND

Cerebrospinal fluid (CSF) tau is a common biomarker for Alzheimer disease (AD). Measurements of tau have historically been performed using immunoassays. Given the molecular diversity of tau in CSF, the selectivity of these immunoassays has often been questioned. Therefore, we aimed to develop an analytically sensitive and selective immunoaffinity liquid chromatography–tandem mass spectrometry (LC-MS/MS) (IA-MS) assay.

METHODS

IA-MS sample analysis involved the addition of an internal standard, immunoaffinity purification of tau using a tau monoclonal antibody coupled to magnetic beads, trypsin digestion, and quantification of a surrogate tau peptide by LC-MS/MS using a Waters Trizaic nanoTile ultraperformance LC microfluidic device. Further characterization of tau peptides was performed by full-scan MS using a Thermo Orbitrap LC-MS. CSF samples from a cohort of age-matched controls and patients with AD were analyzed by the IA-MS method as well as a commercially available immunoassay.

RESULTS

The IA-MS assay had intra- and interassay imprecision values of 3.2% to 8.1% CV and 7.8% to 18.9% C, respectively, a mean recovery of 106%, and a limit of quantification of 0.25 pmol/L and was able to quantify tau concentrations in all human specimens tested. The IA-MS assay showed a correlation of R2 = 0.950 against a total-tau immunoassay. In patients with AD, tau was increased approximately 2-fold.

CONCLUSIONS

Combining immunoaffinity enrichment with microflow LC-MS/MS analysis is an effective approach for the development of a highly selective assay to measure total tau and, potentially, other posttranslationally modified forms of tau in CSF.