Mass spectrometric analysis of neuropeptidergic systems in the human pituitary and cerebrospinal fluid

Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects

Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.

Human Pituitary Adenoma Proteomics: New Progresses and Perspectives

Pituitary adenoma (PA) is a common intracranial neoplasm that impacts on human health through interfering hypothalamus-pituitary-target organ axis systems. The development of proteomics gives great promises in the clarification of molecular mechanisms of a PA and discovery of effective biomarkers for prediction, prevention, early-stage diagnosis, and treatment for a PA. A great progress in the field of PA proteomics has been made in the past 10 years, including (i) the use of laser-capture microdissection, (ii) proteomics analyses of functional PAs (such as prolactinoma), invasive and non-invasive non-functional pituitary adenomas (NFPAs), protein post-translational modifications such as phosphorylation and tyrosine nitration, NFPA heterogeneity, and hormone isoforms, (iii) the use of protein antibody array, (iv) serum proteomics and peptidomics, (v) the integration of proteomics and other omics data, and (vi) the proposal of multi-parameter systematic strategy for a PA. This review will summarize these progresses of proteomics in PAs, point out the existing drawbacks, propose the future research directions, and address the clinical relevance of PA proteomics data, in order to achieve our long-term goal that is use of proteomics to clarify molecular mechanisms, construct molecular networks, and discover effective biomarkers.

Direct cellular peptidomics of hypothalamic neurons

The chemical complexity of cell-to-cell communication has emerged as a fundamental challenge to understanding brain systems. This is certainly true for the hypothalamus, where neuropeptide signals are heterogeneous, localized and dynamic. Thus far, most hypothalamic peptidomic studies have centered on the entire structure; however, recent advances in collection strategies and analytical technologies have enabled direct, high-resolution peptidomic profiles focused on two regions of interest, the suprachiasmatic and supraoptic nuclei, including their sub-regions and individual cells. Suites of peptides now can be identified and probed for function. High spatial and analytical sensitivities reveal that discrete hypothalamic nuclei have distinct peptidomic signatures. Peptidomic discovery not only reveals unanticipated complexity, but also peptides previously unknown that act as key circuit components. Analysis of tissue releasates identifies peptides secreted into the extracellular environment and available for transmitting intercellular signals. Direct sampling techniques define peptide-releasate profiles in spatial, temporal and event-dependent patterns. These approaches are providing remarkable new insights into the complexity of neuropeptidergic cell-to-cell signaling central to neuroendocrine physiology.

Discovery and characterization of the Crustacean hyperglycemic hormone precursor related peptides (CPRP) and orcokinin neuropeptides in the sinus glands of the blue crab Callinectes sapidus using multiple tandem mass spectrometry techniques

The crustacean sinus gland (SG) is a well-defined neuroendocrine site that produces numerous hemolymph-borne agents including the most complex class of endocrine signaling molecules-neuropeptides. Via a multifaceted mass spectrometry (MS) approach, 70 neuropeptides were identified including orcokinins, orcomyotropin, crustacean hyperglycemic hormone (CHH) precursor-related peptides (CPRPs), red pigment concentrating hormone (RPCH), pigment dispersing hormone (PDH), proctolin, RFamides, RYamides, and HL/IGSL/IYRamide. Among them, 15 novel orcokinins, 9 novel CPRPs, 1 novel orcomyotropin, 1 novel Ork/Orcomyotropin-related peptide, and 1 novel PDH were de novo sequenced via collision induced dissociation (CID) from the SG of a model organism Callinectes sapidus. Electron transfer dissociation (ETD) was used for sequencing of intact CPRPs due to their large size and higher charge state. Capillary isoelectric focusing (CIEF) was employed for separation of members of the orcokinin family, which is one of the most abundant neuropeptide families observed in the SG. Collectively, our study represents the most complete characterization of neuropeptides in the SG and provides a foundation for future investigation of the physiological function of neuropeptides in the SG of C. sapidus.

Targeted metabolomics and mass spectrometry

While a great emphasis has been placed on global metabolomic analysis in recent years, the application of metabolomic style analyses to specific subsets of compounds (targeted metabolomics) also has merits in addressing biological questions in a more hypothesis-driven manner. These analyses are designed to selectively extract information regarding a group of related metabolites from the complex mixture of biomolecules present in most metabolomic samples. Furthermore, targeted metabolomics can also be applied to metabolism within macromolecules, hence furthering the systems biology impact of the analysis. This chapter describes the difference between the global metabolomics approach and the undertaking of metabolomics in a targeted manner and describes the application of this type of analysis in a number of biologically and medically relevant fields.

CSF biomarker discovery using label-free nano-LC-MS based proteomic profiling: technical aspects

Biomarker discovery in cerebrospinal fluid (CSF) can provide important information helping to diagnose and monitor disease progression in brain disorders. We present a label-free LC-MS strategy to investigate the proteomic profile of CSF. We provide a framework and protocol addressing quality control, sample replication steps and the adaptation of pattern recognition methods for the detection of experimental variation and (most importantly) putative biomarkers. This strategy was tested using a total of 20 CSF samples (ten samples from healthy volunteers and ten from schizophrenia patients). A clear difference was found between healthy volunteers and schizophrenia patients. With technical and biological variation controlled, we were able to detect 77 proteins with confidence in CSF, of which seven were newly identified, without prior depletion of abundant protein species. Our strategy provides a simple and controlled method for CSF biomarker discovery.

Peptidomics: identification and quantification of endogenous peptides in neuroendocrine tissues

Neuropeptides perform a large variety of functions as intercellular signaling molecules. While most proteomic studies involve digestion of the proteins with trypsin or other proteases, peptidomics studies usually analyze the native peptide forms. Neuropeptides can be studied by using mass spectrometry for identification and quantitation. In many cases, mass spectrometry provides an understanding of the precise molecular form of the native peptide, including post-translational cleavages and other modifications. Quantitative peptidomics studies generally use differential isotopic tags to label two sets of extracted peptides, as done with proteomic studies, except that the Cys-based reagents typically used for quantitation of proteins are not suitable because most peptides lack Cys residues. Instead, a number of amine-specific labels have been created and some of these are useful for peptide quantitation by mass spectrometry. In this review, peptidomics techniques are discussed along with the major findings of many recent studies and future directions for the field.

Comparative proteomics analysis of human pituitary adenomas: current status and future perspectives

This article will review the published research on the elucidation of the mechanisms of pituitary adenoma formation. Mass spectrometry (MS) plays a key role in those studies. Comparative proteomics has been used with the long-term goal to locate, detect, and characterize the differentially expressed proteins (DEPs) in human pituitary adenomas; to identify tumor-related and -specific biomarkers; and to clarify the basic molecular mechanisms of pituitary adenoma formation. The methodology used for comparative proteomics, the current status of human pituitary proteomics studies, and future perspectives are reviewed. The methodologies that are used in comparative proteomics studies of human pituitary adenomas are readily exportable to other different areas of cancer research.

Mass spectrometric characterization of crustacean hyperglycemic hormone precursor-related peptides (CPRPs) from the sinus gland of the crab, Cancer productus

Crustacean hyperglycemic hormone (CHH) precursor-related peptides (CPRPs) are produced during the proteolytic processing of CHH preprohormones. Currently, the physiological roles played by CPRPs are unknown. Due to their large size, direct mass spectrometric sequencing of intact CPRPs is difficult. Here, we describe a novel strategy for sequencing Cancer productus CPRPs directly from a tissue extract using nanoflow liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry. Four novel CPRPs were characterized with the aid of MS/MS de novo sequencing of 27 truncated CPRP peptides. Extensive modifications (methionine oxidation and carboxy-terminal methylation) were identified in both the full-length and truncated peptides. To investigate the origin of the modifications and truncations, a full-length CPRP was synthesized and subjected to the same storage and extraction protocols used for the characterization of the native peptides. Here, some methionine oxidation was seen, however, no methylation or truncation was evident suggesting much of the chemical complexity seen in the native CPRPs is unlikely due to a sample preparation artifact. Collectively, our study represents the most complete characterization of CPRPs to date and provides a foundation for future investigation of CPRP function in C. productus.

Analysis and separation of enkephalin and dalargin analogues and fragments by capillary zone electrophoresis

Capillary zone electrophoresis (CZE) has been applied to qualitative and quantitative analysis and separation of synthetic analogues and fragments of enkephalins ([Leu5]enkephalin, H-Tyr-Gly-Gly-Phe-Leu-OH, [Met5]enkephalin, H-Tyr-Gly-Gly-Phe-Met-OH), and dalargin (H-Tyr-D-Ala-Gly-Phe-Leu-Arg-OH), biologically active peptides with morphin-like effects acting as ligands for the opiate receptors in the brain. These oligopeptides (dipeptides to hexapeptides) were analyzed as cations in two acidic background electrolytes (BGEs), BGE I (100mM H3PO4, 50mM Tris, pH 2.25), BGE II (100mM iminodiacetic acid, pH 2.30), and both as cations and anions in alkaline BGE IV (40 mM Tris, 40 mM Tricine, pH 8.10). Purity degrees of peptides, expressed in three different ways (relative peak height, relative peak area and relative corrected peak area), were determined by their CZE analyses in the above BGEs, and their values were compared with respect to the peak shapes and migration times of the main synthetic products and their admixtures. Selected analogues and fragments of enkephalins and dalargin were successfully separated by CZE in acidic isoelectric buffers, 100 and 200 mM iminodiacetic acid, pH 2.30 and 2.32, respectively. The effective electrophoretic mobilities at standard temperature 25 degrees C, and effective and specific charges of all analyzed peptides in the above three BGEs were determined. Correlation between effective electrophoretic mobility of the analyzed peptides and their charge and size (relative molecular mass) was investigated, which revealed different molecular shape of analyzed peptides in acidic and alkaline BGEs. In addition, the selected characteristics of the UV-absorption detector (noise, signal to noise ratio, sensitivity, and limits of detection and quantification) were determined.

Quantitative Neuropeptidomics of Microwave-irradiated Mouse Brain and Pituitary

In neuropeptidomics, the degradation of a small fraction of abundant proteins overwhelms the low signals from neuropeptides, and many neuropeptides cannot be detected by mass spectrometry without extensive purification. Protein degradation was prevented when mice were sacrificed with focused microwave irradiation, permitting the detection of hypothalamic neuropeptides by mass spectrometry. Here we report an alternative and very simple method utilizing an ordinary microwave oven to inhibit enzymatic degradation. We used this technique to identify brain and pituitary neuropeptides. Quantitative analysis using mass spectrometry in combination with stable isotopic labeling was performed to determine the effect of microwave irradiation on relative levels of neuropeptides and protein degradation fragments. Microwave irradiation greatly reduced the levels of degradation fragments of proteins. In contrast, neuropeptide levels were increased about 2-3 times in hypothalamus by the microwave irradiation but not increased in pituitary. In a second experiment, three brain regions (hypothalamus, hippocampus, and striatum) from microwave-irradiated mice were analyzed. Altogether 41 neuropeptides or fragments of secretory pathway proteins were identified after microwave treatment; some of these are novel. These peptides were derived from 15 proteins: proopiomelanocortin, proSAAS, proenkephalin, preprotachykinins A and B, provasopressin, prooxytocin, melanin-concentrating hormone, proneurotensin, chromogranins A and B, secretogranin II, prohormone convertases 1 and 2, and peptidyl amidating monooxygenase. Although some protein degradation fragments were still found after microwave irradiation, these appear to result from protein breakdown during the extraction and not to an enzymatic reaction during the postmortem period. Two of the protein fragments corresponded to novel protein forms: VAP-33 with a 7-residue N-terminal extension and beta tubulin with a glutathione on the Cys near the N terminus. In conclusion, microwave irradiation with an ordinary microwave oven effectively inhibits enzymatic postmortem protein degradation, increases the recovery of neuropeptides, and makes it possible to conduct neuropeptidomic studies with mouse brain tissues.

A new member of the hypothalamic RF-amide peptide family, LPXRF-amide peptides: structure, localization, and function

Recently, we identified a novel hypothalamic neuropeptide with a C-terminal LPLRF-amide sequence in the quail brain. This avian neuropeptide was shown to inhibit gonadotropin release from the cultured anterior pituitary. This peptide is the first hypothalamic peptide that inhibited gonadotropin release reported in vertebrates. We, therefore, termed it gonadotropin-inhibitory hormone (GnIH). After this finding, we found that GnIH-related peptides were present in the brains of other vertebrates, such as mammals, amphibians, and fish. These GnIH-related peptides possessed a LPXRF-amide (X=L or Q) motif at their C-termini in all investigated animals. Mass spectrometric analyses combined with immunoaffinity chromatography were powerful techniques for the identification of mature endogenous LPXRF-amide peptides. The identified LPXRF-amide peptides were found to be localized in the hypothalamus and brainstem areas, and to regulate pituitary hormone release. Subsequently, cDNAs that encode LPXRF-amide peptides were characterized in vertebrate brains. In this review, we summarize the identification, localization, and function of a new member of the hypothalamic RF-amide peptide family, LPXRF-amide peptides in vertebrates. Recent studies on the receptors for LPXRF-amide peptides will also be reviewed.

Plasma Protein Profiling for Diagnosis of Pancreatic Cancer Reveals the Presence of Host Response Proteins

Plasma protein profiling using separations coupled to matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) has great potential in translational research; it can be used for biomarker discovery and contribute to disease diagnosis and therapy. Previously reported biomarker searches have been done solely by MS protein profiling followed by bioinformatics analysis of the data. To add to current methods, we tested an alternative strategy for plasma protein profiling using pancreatic cancer as the model. First, offline solid-phase extraction is done with 96-well plates to fractionate and partially purify the proteins. Then, multiple profiling and identification experiments can be conducted on the same protein fractions because only 5% of the fractions are used for MALDI MS profiling. After MALDI MS analysis, the mass spectra are normalized and subjected to a peak detection algorithm. Over three sets of mass spectra acquired using different instrument variables, ∼400 unique ion signals were detected. Classification schemes employing as many as eight individual peaks were developed using a training set with 123 members (82 cancer patients) and a blinded validation set with 125 members (57 cancer patients). The sensitivity of the study was 88%, but the specificity was significantly lower, 75%. The reason for the low specificity becomes apparent upon protein identification of the ion signals used for the classification. The identifications reveal only common serum proteins and components of the acute phase response, including serum amyloid A, α-1-antitrypsin, α-1-antichymotrypsin, and inter-α-trypsin inhibitor.

Quantitative peptidomics of mouse pituitary: comparison of different stable isotopic tags

Determining the relative levels of neuropeptides in two samples is important for many biological studies. An efficient, sensitive and accurate technique for relative quantitative analysis involves tagging the peptides in the two samples with isotopically distinct labels, pooling the samples and analyzing them using liquid chromatography/mass spectrometry (LC/MS). In this study, we compared two different sets of isotopic tags for analysis of endogenous mouse pituitary peptides: succinic anhydride with either four hydrogens or deuteriums and [3-(2,5-dioxopyrrolidin-1-yloxycarbonyl)propyl]trimethylammonium chloride with either nine hydrogens or deuteriums. These two labels react with amines and impart either a negative charge (succinyl) or a positive charge (4-trimethylammoniumbutyryl (TMAB)). Every endogenous mouse pituitary peptide labeled with the light TMAB reagent eluted from the C18 reversed-phase column at essentially the same time as the corresponding peptide labeled with the heavy reagent. Most of the peptides labeled with succinyl groups also showed co-elution of the heavy- and light-labeled forms on LC/MS. The mass difference between the heavy and light TMAB reagents (9 Da per label) was larger than that of the heavy and light succinyl labels (4 Da per label), and for some peptides the larger mass difference provided more accurate determination of the relative abundance of each form. Altogether, using both labels, 82 peptides were detected in Cpe(fat/fat) mouse pituitary extracts. Of these, only 16 were detected with both labels, 41 were detected only with the TMAB label and 25 were detected only with the succinyl label. A number of these peptides were de novo sequenced using low-energy collisional tandem mass spectrometry. Whereas the succinyl group was stable to the collision-induced dissociation of the peptide, the TMAB-labeled peptides lost 59 Da per H9 TMAB group. Several peptides identified in this analysis represent previously undescribed post-translational processing products of known pituitary prohormones. In conclusion, both succinyl and TMAB isotopic labels are useful for quantitative peptidomics, and together these two labels provide more complete coverage of the endogenous peptides.

A novel mass spectrometric approach to the analysis of hormonal peptides in extracts of mouse pancreatic islets

Liquid chromatography mass spectrometry (LC-MS) is a valuable tool in the analysis of proteins and peptides. The combination of LC-MS with different fragmentation methods provides sequence information on components in complex mixtures. In this work, on-line packed capillary LC electrospray ionization Fourier transform ion cyclotron resonance MS was combined with two complementary fragmentation techniques, i.e. nozzle-skimmer fragmentation and electron capture dissociation, for the determination of hormonal peptides in an acid ethanol extract of mouse pancreatic islets. The most abundant peptides, those derived from proinsulin and proglucagon, were identified by their masses and additional sequence-tag information established their identities. Interestingly, the experiments demonstrated the presence of truncated C-peptides, des-(25-29)-C-peptide and des-(27-31)-C-peptide. These novel findings clearly illustrate the potential usefulness of the described technique for on-line sequencing and characterization of peptides in tissue extracts.

Application of a C-peptide electrospray ionization-isotope dilution-liquid chromatography-tandem mass spectrometry measurement procedure for the evaluation of five C-peptide immunoassays for urine

This study applied electrospray ionization-isotope dilution-liquid chromatography-tandem mass spectrometry for the evaluation of five urinary C-peptide immunoassays via split-sample measurements. The immunoassays measured in duplicate in the same run, the comparison method in triplicate over different runs. From the data, the within-run imprecision and the method comparison total RSDs were calculated. Regression analysis revealed on the one hand systematic differences, on the other, an excellent correlation between the test and comparison methods. From the spread of the data around the regression line in comparison with the 95% prediction intervals from the total RSD, sample-related effects and/or specificity problems were apparent and investigated.

Proteomics and transcriptomics analyses of secretagogin down-regulation in human non-functional pituitary adenomas

In order to explore the presence of, and the potential role of, secretagogin in human pituitary adenomas, an analytical strategy that integrated comparative proteomics and comparative transcriptomics was used to detect the protein and the mRNA expression, respectively, of secretagogin in human non-functional pituitary adenomas compared to controls. Proteomics methods included two-dimensional gel electrophoresis, 2D gel image analysis, mass spectrometry [matrix-assisted laser desorption/ionization-time of flight-peptide mass fingerprinting (MALDI-TOF PMF) and liquid chromatography-electrospray ionization-quadrupole-ion trap tandem mass spectrometry (LC-ESI-Q-IT MS/MS)], and database analysis. Transcriptomics methods included the GeneChip microarray, image processing, and data analysis. The proteomics and transcriptomics data demonstrated that secretagogin was significantly down-regulated at the protein and mRNA levels, respectively, in the human non-functional (NF) pituitary adenomas (NF-, LH+, FSH+, and FSH+ + LH+). For the secretagogin protein, the expression level was NF- < FSH+ + LH+ < FSH+ < LH+ < Control, with a range of down-regulation of 2.2-6.9 fold in non-functional pituitary adenomas compared to controls, with a significant difference (p < 0.001). For secretagogin mRNA, the expression level was NF- < LH+ < FSH+ + LH+ < FSH+ < Control, with a range of down-regulation of 1.8-18.6 fold in non-functional pituitary adenomas compared to controls that was significant (p < 0.05). The secretagogin protein expression correlated significantly with its mRNA expression. Those results suggest that secretagogin might play a role in human non-functional pituitary adenomas. This novel finding may provide clues to clarify the basic molecular mechanisms of pituitary adenoma formation, and to identify new tumor-related markers.

High-resolution peptide mapping of cerebrospinal fluid: a novel concept for diagnosis and research in central nervous system diseases

Peptides, such as many hormones, cytokines and growth factors play a central role in biological processes. Furthermore, as degradation products and processed forms of larger proteins they are part of the protein turnover. Thus, they can reflect disease-related changes in an organism's homeostasis in several ways. Since two-dimensional gel electrophoresis is restricted to analysis and display of proteins with relative molecular masses above 5000, we developed Differential Peptide Display (DPD), a new technology for analysis and visualization of peptides. Here we describe its application to cerebrospinal fluid of three subjects without a disease of the central nervous system (CNS) undergoing routine myelography and of two patients suffering from a primary CNS lymphoma. Peptides with a relative molecular mass below 20000 were extracted and analysed by a combination of chromatography and mass spectrometry. The peptide pattern of a sample was depicted as a multi-dimensional peptide mass fingerprint with each peptide's position being characterized by its molecular mass and chromatographic behaviour. Such a fingerprint of a CNS sample consists of more than 6000 different signals. Data analysis of peptide patterns from patients with CNS lymphoma compared to controls revealed obvious differences regarding the peptide content of the samples. By analysing peptides within a mass range of 750-20000, DPD extends 2D gel electrophoresis, thus offering the chance to investigate CNS diseases on the level of peptides. This represents a new approach for diagnosis and possible therapy.

Peptide repertoire of human cerebrospinal fluid: novel proteolytic fragments of neuroendocrine proteins

Polypeptides in human cerebrospinal fluid (CSF), isolated by phase separation in chloroform-methanol-water and reversed-phase HPLC, were characterised by sequence analysis and mass spectrometry. This identified the presence of peptide fragments of testican, neuroendocrine specific protein VGF, neuroendocrine protein 7B2, chromogranin B/secretogranin I, chromogranin A, osteopontin, IGF-II E-peptide and proenkephalin. The majority of these fragments were generated by proteolysis at dibasic sites, suggesting that they are derived by activities related to prohormone convertase(s). Several of the fragments have previously not been detected, and their functions in CSF or elsewhere are unknown. A characteristic feature of all these fragments is a very high content of acidic residues, in particular glutamic acid. In addition to the fragments of neuroendocrine proteins, endothelin-binding receptor-like protein 2, ribonuclease 1, IGF-binding protein 6, albumin, alpha1-acid glycoprotein 1, prostaglandin-H2 D-isomerase, apolipoprotein A1, transthyretin, beta2-microglobulin, ubiquitin, fibrinopeptide A, and C4A anaphylatoxin were found.