Biochemically identified neuropeptides in a caddisfly (Trichoptera) and a pygmy mole cricket (Orthoptera: Caelifera: Tridactyloidea).

One representative of the order Trichoptera, namely the caddisfly Chaetopteryx villosa, was investigated along with the pygmy mole cricket Xya capensis which is a representative of the most basal superfamily of the caeliferan Orthoptera, that is, the Tridactyloidea. From both clades neuropeptides have not been biochemically characterized before this study. Here, members of the adipokinetic hormone family (AKHs) are sequenced via liquid chromatography (LC)-ion trap mass spectrometry from methanolic extracts from the corpora cardiaca of respective species. The corpora cardiaca were dissected, methanolic extracts prepared, peptides separated by liquid chromatography (LC), and AKHs detected and sequenced by ion trap mass spectrometry. Both species investigated contain an octapeptide AKH: the trichopteran species has the peptide with the sequence pGlu-Leu-Thr-Phe-Thr-Pro-Ser-Trp amide; the ambiguity of the isobaric amino acids Leu and Ile at position two was solved by comparing retention times on LC and by co-elution with the synthetic Leu2 -form. This peptide is known as Aedae-AKH and found in certain dipteran species and in an alderfly (Megaloptera). The tridactyloid species contains the peptide with the sequence pGlu-Val-Asn-Phe-Ser-Pro-Gly-Trp amide which had first been identified in a member of the order Mantophasmatodea and is called Manto-CC. Comparisons are made between the AKH complements of the sister groups Trichoptera and Lepidoptera and their possible relatedness and, on the other hand, between the AKH of X. capensis with those of closely related caeliferan superfamilies. The biology of the two studied species is used to speculate about a possible function of the elucidated hormones. Lastly, the use of a larval stage as starting material for structural neuropeptide information is discussed.

Purification and identification of native forms of goldfish neuromedin U from brain and gut.

Neuromedin U (NMU) plays important roles in energy homeostasis in rodents and birds. Previously, our group has isolated four cDNAs encoding precursor proteins of NMU from the goldfish brain and gut, and it was assumed that these transcripts are produced by alternative splicing. We have also demonstrated that intracerebroventricular (ICV) injection of putative goldfish NMU inhibits food intake. However, as native goldfish NMU has not yet been identified, we attempted to purify it from goldfish brain and gut extracts. To assess NMU activity in fractions at each purification step, we measured changes in the intracellular concentrations of Ca2+ using HEK293 cells expressing goldfish NMU-R1 or -R2. We isolated a 25-amino-acid peptide (NMU-25) from the brain and gut and found that its primary structure is similar to that of mammalian NMU. Another 21-amino-acid peptide (NMU-21) was purified from the brain, but not from the gut. Furthermore, a 9-amino-acid peptide (NMU-9) identical to the C-terminus of NMU-21 and -25 was also isolated from the brain and gut. Treatment with synthetic NMU-9, -21 and -25 dose-dependently increased the intracellular Ca2+ concentration in mammalian cells expressing goldfish NMU-R1 and -R2. We also examined the effect of ICV-administered synthetic goldfish NMUs on goldfish food intake. NMU-25 inhibited food intake to the same degree as NMU-21. However, the inhibitory effect of NMU-9 was slightly weaker than those of NMU-21 and -25. These results indicate that several molecular forms of NMU exist in the goldfish brain and gut, and that all of them play physiological roles via NMU-R1 and NMU-R2.

Production of polyclonal antibody against human Neuritin and its application of immunodetection.

OBJECTIVE: To date, a commercial antibody to human Neuritin for immunoprecipitation is still limited. In this study, we aimed to develop a specific antibody for further research on the potential function of Neuritin. METHODS AND RESULTS: By epitope prediction of recombinant human Neuritin, the active fragment of human Neuritin that could be used as an excellent immunogen. Soluble His-tagged Neuritin was expressed and purified from Pichia pastoris. Polyclonal antibody against Neuritin was obtained by immunizing Sprague-Dawley rats with purified recombinant human Neuritin. Affinity-purified polyclonal antibody against Neuritin was characterized with indirect enzyme-linked immunosorbent assay, immunoblotting, immunoprecipitation, and immunofluorescence. The results demonstrated that the polyclonal antibody against Neuritin had been prepared successfully. The prepared antibody bound to both exogenous and endogenous Neuritin. Importantly, the anti-Neuritin polyclonal antibody could be used in immunoprecipitation assays. CONCLUSIONS: The prepared polyclonal antibody could be used in immunoprecipitation and provide researchers with a useful tool for further investigating the function and mechanism of Neuritin.

Separation and identification of mouse brain tissue microproteins using top-down method with high resolution nanocapillary liquid chromatography mass spectrometry.

Microproteins and endogenous peptides in the brain contain important substances that have critical roles in diverse biological processes, contributing to signal transduction and intercellular signaling. However, variability in their physical or chemical characteristics, such as molecule size, hydrophobicity, and charge states, complicate the simultaneous analysis of these compounds, although this would be highly beneficial for the field of neuroscience research. Here, we present a top-down analytical method for simultaneous analysis of microproteins and endogenous peptides using high-resolution nanocapillary LC-MS/MS. This method is detergent-free and digestion-free, which allows for extracting and preserving intact microproteins and peptides for direct LC-MS analysis. Both higher energy collision dissociation and electron-transfer dissociation fragmentations were used in the LC-MS analysis to increase the identification rate, and bioinformatics tools ProteinGoggle and PEAKS Studio software were utilized for database search. In total, we identified 471 microproteins containing 736 proteoforms, including brain-derived neurotrophic factor and a number of fibroblast growth factors. In addition, we identified 599 peptides containing 151 known or potential neuropeptides such as somatostatin-28 and neuropeptide Y. Our approach bridges the gap for the characterization of brain microproteins and peptides, which permits quantification of a diversity of signaling molecules for biomarker discovery or therapy diagnosis in the future.

Localization of Drebrin: Light Microscopy Study.

Developmental changes in the expression and localization of drebrin has been mainly analyzed in chick embryo and young rat by various anti-drebrin polyclonal and monoclonal antibodies. Immunoblot analysis demonstrated that the adult drebrin isoform (drebrin A) is restricted to neural tissues, while the embryonic drebrin isoforms (drebrin E1 and E2 in chicken and drebrin E in mammals) are found in a wide variety of tissues. In the developing brain, drebrin E (including chicken drebrin E2) is expressed in newly generated neurons. During neuronal migration, drebrin E is distributed ubiquitously within the neurons. Once drebrin A is expressed in the developing neuron, drebrin E is no longer present within the cell soma and accumulates in the growth cone of growing processes, resulting in the cessation of neuronal migration. The limited subcellular localization of drebrin A, which is possibly regulated by a drebrin A-specific mechanism, is likely to affect the localization of drebrin E. In the adult brain, drebrin is mainly localized in dendritic spines, but in some nuclei, drebrin can be detected in neuronal somata as well as dendritic spines. The fact that the developmental changes in drebrin expression highly correlate in time with the sensitive period of visual cortical plasticity in kittens suggests that synaptic plasticity depends on drebrin.

Fast and Reliable Quantitative Peptidomics with labelpepmatch.

The use of stable isotope tags in quantitative peptidomics offers many advantages, but the laborious identification of matching sets of labeled peptide peaks is still a major bottleneck. Here we present labelpepmatch, an R-package for fast and straightforward analysis of LC-MS spectra of labeled peptides. This open-source tool offers fast and accurate identification of peak pairs alongside an appropriate framework for statistical inference on quantitative peptidomics data, based on techniques from other -omics disciplines. A relevant case study on the desert locust Schistocerca gregaria proves our pipeline to be a reliable tool for quick but thorough explorative analyses.

Identification of a novel starfish neuropeptide that acts as a muscle relaxant.

Neuropeptides that act as muscle relaxants have been identified in chordates and protostomian invertebrates but little is known about the molecular identity of neuropeptides that act as muscle relaxants in deuterostomian invertebrates (e.g. echinoderms) that are 'evolutionary intermediates' of chordates and protostomes. Here, we have used the apical muscle of the starfish Patiria pectinifera to assay for myorelaxants in extracts of this species. A hexadecapeptide with the amino acid sequence Phe-Gly-Lys-Gly-Gly-Ala-Tyr-Asp-Pro-Leu-Ser-Ala-Gly-Phe-Thr-Asp was identified and designated starfish myorelaxant peptide (SMP). Cloning and sequencing of a cDNA encoding the SMP precursor protein revealed that it comprises 12 copies of SMP as well as 3 peptides (7 copies in total) that are structurally related to SMP. Analysis of the expression of SMP precursor transcripts in P. pectinifera using qPCR revealed the highest expression in the radial nerve cords and lower expression levels in a range of neuromuscular tissues, including the apical muscle, tube feet and cardiac stomach. Consistent with these findings, SMP also caused relaxation of tube foot and cardiac stomach preparations. Furthermore, SMP caused relaxation of apical muscle preparations from another starfish species - Asterias amurensis. Collectively, these data indicate that SMP has a general physiological role as a muscle relaxant in starfish. Interestingly, comparison of the sequence of the SMP precursor with known neuropeptide precursors revealed that SMP belongs to a bilaterian family of neuropeptides that include molluscan pedal peptides (PP) and arthropodan orcokinins (OK). This is the first study to determine the function of a PP/OK-type peptide in a deuterostome. Pedal peptide/orcokinin (PP/OK)-type peptides are a family of structurally related neuropeptides that were first identified and functionally characterised in protostomian invertebrates. Here, we report the discovery of starfish myorelaxant peptide (SMP), a novel member of the PP/OK-type neuropeptide identified in the starfish Patiria pectinifera (phylum Echinodermata). SMP is the first PP/OK-type neuropeptide to be functionally characterised in a deuterostome.

Dynamic-Electromembrane Extraction: A Technical Development for the Extraction of Neuropeptides.

In this work, a dynamic-electromembrane extraction (d-EME) device was developed for the extraction of neuropeptides. On the basis of a thin polypropylene hollow fiber (50 µm of wall-thickness and 280 µm i.d.), this setup allowed for a continual renewal of the acceptor compartment. Because of the reduced size of the device, high preconcentration factors were obtained (up to 50-fold). The extraction remained constant regardless of the extraction time (from 15 to 45 min); accordingly, this new setup minimized the effect of electrolysis on extraction performance while enabling high extraction yield (up to 72%) for most lipophilic neuropeptides.

Identification and bioactivity evaluation of the first neuropeptide from the lesser-known insect order Embioptera (webspinner).

A species of the poorly studied order Embioptera, the webspinner Oligotoma saundersii, is investigated for its complement of neuropeptides of the adipokinetic hormone (AKH) family. A methanolic extract of its corpora cardiaca (CC) is able to effect carbohydrate mobilization in the cockroach, Periplaneta americana, and liquid chromatography coupled to electrospray ionization mass spectrometry clearly identified one decapeptide as a member of the AKH family in the CC of O. saundersii. The primary structure of this peptide, code-named Olisa-AKH, is elucidated as pEVNFSPNWGG amide. It is a novel member of the AKH family and in its synthetic form it has strong hypertrehalosemic activity in the American cockroach. This effect may be explained by its near-identical structure compared with one of the endogenous cockroach AKH peptides. An analog with the reversed order of the proline and asparagine residues, viz. N(6)P(7)-Olisa-AKH, had negligible activity thus, shedding light on the requirements of the cockroach AKH receptor. From reversed-phase high-performance liquid chromatography experiments, we can conclude that the CC from an individual webspinner contains less than one pmol of Olisa-AKH. Comparison of the AKH sequences from the major orders of the Polyneoptera does not point to a close phylogenetic relationship between webspinners and stick insects.

Quantitative Neuropeptidome Analysis Reveals Neuropeptides Are Correlated with Social Behavior Regulation of the Honeybee Workers.

Neuropeptides play vital roles in orchestrating neural communication and physiological modulation in organisms, acting as neurotransmitters, neuromodulators, and neurohormones. The highly evolved social structure of honeybees is a good system for understanding how neuropeptides regulate social behaviors; however, much knowledge on neuropeptidomic variation in the age-related division of labor remains unknown. An in-depth comparison of the brain neuropeptidomic dynamics over four time points of age-related polyethism was performed on two strains of honeybees, the Italian bee (Apis mellifera ligustica, ITb) and the high royal jelly producing bee (RJb, selected for increasing royal jelly production for almost four decades from the ITb in China). Among the 158 identified nonredundant neuropeptides, 77 were previously unreported, significantly expanding the coverage of the honeybee neuropeptidome. The fact that 14 identical neuropeptide precursors changed their expression levels during the division of labor in both the ITb and RJb indicates they are highly related to task transition of honeybee workers. These observations further suggest the two lines of bees employ a similar neuropeptidome modification to tune their respective physiology of age polyethism via regulating excretory system, circadian clock system, and so forth. Noticeably, the enhanced level of neuropeptides implicated in regulating water homeostasis, brood pheromone recognition, foraging capacity, and pollen collection in RJb signify the fact that neuropeptides are also involved in the regulation of RJ secretion. These findings gain novel understanding of honeybee neuropeptidome correlated with social behavior regulation, which is potentially important in neurobiology for honeybees and other insects.

Defining the Neuropeptidome of the Spiny Lobster Panulirus interruptus Brain Using a Multidimensional Mass Spectrometry-Based Platform.

Decapod crustaceans are important animal models for neurobiologists due to their relatively simple nervous systems with well-defined neural circuits and extensive neuromodulation by a diverse set of signaling peptides. However, biochemical characterization of these endogenous neuropeptides is often challenging due to limited sequence information about these neuropeptide genes and the encoded preprohormones. By taking advantage of sequence homology in neuropeptides observed in related species using a home-built crustacean neuropeptide database, we developed a semi-automated sequencing strategy to characterize the neuropeptidome of Panulirus interruptus, an important aquaculture species, with few known neuropeptide preprohormone sequences. Our streamlined process searched the high mass accuracy and high-resolution data acquired on a LTQ-Orbitrap with a flexible algorithm in ProSight that allows for sequence discrepancy from reported sequences in our database, resulting in the detection of 32 neuropeptides, including 19 novel ones. We further improved the overall coverage to 51 neuropeptides with our multidimensional platform that employed multiple analytical techniques including dimethylation-assisted fragmentation, de novo sequencing using nanoliquid chromatography-electrospray ionization-quadrupole-time-of-flight (nanoLC-ESI-Q-TOF), direct tissue analysis, and mass spectrometry imaging on matrix-assisted laser desorption/ionization (MALDI)-TOF/TOF. The high discovery rate from this unsequenced model organism demonstrated the utility of our neuropeptide discovery pipeline and highlighted the advantage of utilizing multiple sequencing strategies. Collectively, our study expands the catalog of crustacean neuropeptides and more importantly presents an approach that can be adapted to exploring neuropeptidome from species that possess limited sequence information.

Expression and purification of recombinant human neuritin from Pichia pastoris and a partial analysis of its neurobiological activity in vitro.

Neuritin (also known as candidate plasticity gene 15 (cpg15)) is a neurotrophic factor that was recently discovered in a screen aimed at identifying genes involved in activity-dependent synaptic plasticity. Neuritin plays multiple roles in both neural development (Chen et al. Zhonghua Yan Ke Za Zhi 46:978-983 2010; Corriveau et al. J Neurosci 19:7999-8008 1999; Lee and Nedivi J Neurosci 22:1807-1815 2002) and synaptic plasticity (Fujino et al. Gene Dev 25:2674-2685 2011; Leslie and Nedivi Prog 14 Neurobiol 94:223-237 2011; Loebrich and Nedivi Physiol Rev 89:1079 2009). In this study, to produce bioactive, soluble recombinant human neuritin protein, a portion of NRN1 was cloned into the Pichia pastoris expression vector pPIC9K. The recombinant vector was then transformed into the methylotrophic yeast strain P. pastoris GS115, and a shaking flask method and His-tag purification strategy were utilized to express and purify neuritin protein. The resulting protein had a molecular mass of approximately 11 kDa, and subsequent functional analyses indicated that the purified neuritin promoted neurite outgrowth from embryonic chicken dorsal root ganglions, while also prolonging the survival of these ganglions, and from PC12 cells. These findings suggest that neuritin was expressed effectively in vitro and that this protein may play a role in stimulating neurite outgrowth of both dorsal root ganglions and PC12 cells. This study provides a novel strategy for the large-scale production of bioactive neuritin, which will enable further study of the biological function of this protein.

Chronic nicotine treatment impacts the regulation of opioid and non-opioid peptides in the rat dorsal striatum.

The chronic use of nicotine, the main psychoactive ingredient of tobacco smoking, alters diverse physiological processes and consequently generates physical dependence. To understand the impact of chronic nicotine on neuropeptides, which are potential molecules associated with dependence, we conducted qualitative and quantitative neuropeptidomics on the rat dorsal striatum, an important brain region implicated in the preoccupation/craving phase of drug dependence. We used extensive LC-FT-MS/MS analyses for neuropeptide identification and LC-FT-MS in conjunction with stable isotope addition for relative quantification. The treatment with chronic nicotine for 3 months led to moderate changes in the levels of endogenous dorsal striatum peptides. Five enkephalin opioid peptides were up-regulated, although no change was observed for dynorphin peptides. Specially, nicotine altered levels of nine non-opioid peptides derived from precursors, including somatostatin and cerebellin, which potentially modulate neurotransmitter release and energy metabolism. This broad but selective impact on the multiple peptidergic systems suggests that apart from the opioid peptides, several other peptidergic systems are involved in the preoccupation/craving phase of drug dependence. Our finding permits future evaluation of the neurochemical circuits modulated by chronic nicotine exposure and provides a number of novel molecules that could serve as potential therapeutic targets for treating drug dependence.

Preparation and application of a novel molecularly imprinted solid-phase microextraction monolith for selective enrichment of cholecystokinin neuropeptides in human cerebrospinal fluid.

A novel molecularly imprinted polymer (MIP) monolith for highly selective extraction of cholecystokinin (CCK) neuropeptides was prepared in a micropipette tip. The MIPs were synthesized by epitope imprinting technique and the polymerization conditions were investigated and optimized. The synthesized MIPs were characterized by infrared spectroscopy, elemental analyzer and scanning electron microscope. A molecularly imprinted solid-phase microextraction (MI-µ-SPE) method was developed for the extraction of CCK neuropeptides in aqueous solutions. The parameters affecting MI-µ-SPE were optimized. The results indicated that this MIP monolith exhibited specific recognition capability and high enrichment efficiency for CCK neuropeptides. In addition, it showed excellent reusability. This MIP monolith was used for desalting and enrichment of CCK4, CCK5 and CCK8 from human cerebrospinal fluid prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis, and the results show that this MIP monolith can be a useful tool for effective purification and highly selective enrichment of multiple homologous CCK neuropeptides in cerebrospinal fluid simultaneously. By employing MI-µ-SPE combined with HPLC-ESI-MS/MS analysis, endogenous CCK4 in human cerebrospinal fluid was quantified.

Quantitative neuropeptidomics study of the effects of temperature change in the crab Cancer borealis.

Temperature changes influence the reaction rates of all biological processes, which can pose dramatic challenges to cold-blooded organisms, and the capability to adapt to temperature fluctuations is crucial for the survival of these animals. In order to understand the roles that neuropeptides play in the temperature stress response, we employed a mass spectrometry-based approach to investigate the neuropeptide changes associated with acute temperature elevation in three neural tissues from the Jonah crab Cancer borealis. At high temperature, members from two neuropeptide families, including RFamide and RYamide, were observed to be significantly reduced in one of the neuroendocrine structures, the pericardial organ, while several orcokinin peptides were detected to be decreased in another major neuroendocrine organ, the sinus gland. These results implicate that the observed neuropeptides may be involved with temperature perturbation response via hormonal regulation. Furthermore, a temperature stress marker peptide with the primary sequence of SFRRMGGKAQ (m/z 1137.7) was detected and de novo sequenced in the circulating fluid (hemolymph) from animals under thermal perturbation.

Recent advances in quantitative neuroproteomics.

The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.

[Prokineticins: new regulatory peptides in human reproduction]. / Prokinéticines - De nouveaux peptides régulateurs de la reproduction humaine.

During the last decade, there has been growing evidence for the involvement of prokineticins and their receptors (PROK/PROKR) in human reproduction, with multiple roles in the female and male reproductive systems. The PROK/PROKR signalling complex has been reported as a new actor in ovary, uterus, placenta, and testis physiology, with marked dysfunction in various pathological conditions such as polycystic ovary syndrome, recurrent pregnancy loss, preeclampsia, and ectopic pregnancy. Altogether, the results strongly suggest the involvement of prokineticins in spermatogenesis, oocyte competence, embryo implantation, pregnancy, and delivery, and argue for the clinical relevance of these cytokines and their receptors as diagnostic markers for several reproductive diseases.

Isolation and characterization of NGFFYamide neuropeptide from Patiria pectinifera pyloric caeca extract.

Neuropeptides are small molecules that mediate intercellular signaling and regulate physiological processes. Starfish possess various myoactive neuropeptides, including starfish myorelaxant peptide (SMP) and a calcitonin-type peptide with apical muscle relaxing properties. In this study, we report the purification of a neuropeptide from starfish (Patiria pectinifera) pyloric caeca extract using high-performance liquid chromatography (HPLC) and an in vitro bioassay to screen for fractions and peptides with relaxing effects on P. pectinifera apical muscle preparations. A series of HPLC steps using reversed-phase and cation-exchange columns yielded a purified peptide with muscle-relaxing effects. The purified peptide's structure was determined by LC-MS and Edman degradation, revealing a pentapeptide with an amidated C-terminus (NGFFYamide) and a molecular mass of 646.2930 Da. This is the first report of NGFFYamide purification from P. pectinifera through biochemical methods. The nucleotide sequence encoding the NGFFYamide precursor was determined, showing the presence of a conserved neurophysin domain in the C-terminal region. RT-qPCR results confirmed high expression in radial nerves cord, consistent with previous findings on NG peptides in echinoderms. In vitro pharmacological studies on muscle preparations from P. pectinifera and Asterias amurensis revealed differential relaxing activity of NGFFYamide on apical muscles, while its effects on tube foot preparations were similar in both species. NGFFYamide also induced potent contraction in P. pectinifera cardiac stomach. Comparison of three NG peptides (NGFFYamide, NGFFFamide, and NGIWYamide) on P. pectinifera cardiac stomach revealed varying potency, suggesting class-specific receptor interactions. Tachyphylaxis was observed in P. pectinifera apical muscle but not in A. amurensis, warranting further investigation. Based on these results, it is plausible that NGFFYamide could be involved in regulating locomotion and feeding behavior in P. pectinifera, consistent with findings in Asterias rubens.

Standardized protocols for quality control of MRM-based plasma proteomic workflows.

Mass spectrometry (MS)-based proteomics is rapidly emerging as a viable technology for the identification and quantitation of biological samples, such as human plasma--the most complex yet commonly employed biofluid in clinical analyses. The transition from a qualitative to quantitative science is required if proteomics is going to successfully make the transition to a clinically useful technique. MS, however, has been criticized for a lack of reproducibility and interlaboratory transferability. Currently, the MS and plasma proteomics communities lack standardized protocols and reagents to ensure that high-quality quantitative data can be accurately and precisely reproduced by laboratories across the world using different MS technologies. Toward addressing this issue, we have developed standard protocols for multiple reaction monitoring (MRM)-based assays with customized isotopically labeled internal standards for quality control of the sample preparation workflow and the MS platform in quantitative plasma proteomic analyses. The development of reference standards and their application to a single MS platform is discussed herein, along with the results from intralaboratory tests. The tests highlighted the importance of the reference standards in assessing the efficiency and reproducibility of the entire bottom-up proteomic workflow and revealed errors related to the sample preparation and performance quality and deficits of the MS and LC systems. Such evaluations are necessary if MRM-based quantitative plasma proteomics is to be used in verifying and validating putative disease biomarkers across different research laboratories and eventually in clinical laboratories.

Improving the identification rate of endogenous peptides using electron transfer dissociation and collision-induced dissociation.

Tandem mass spectrometry (MS/MS) combined with bioinformatics tools have enabled fast and systematic protein identification based on peptide-to-spectrum matches. However, it remains challenging to obtain accurate identification of endogenous peptides, such as neuropeptides, peptide hormones, peptide pheromones, venom peptides, and antimicrobial peptides. Since these peptides are processed at sites that are difficult to predict reliably, the search of their MS/MS spectra in sequence databases needs to be done without any protease setting. In addition, many endogenous peptides carry various post-translational modifications, making it essential to take these into account in the database search. These characteristics of endogenous peptides result in a huge search space, frequently leading to poor confidence of the peptide characterizations in peptidomics studies. We have developed a new MS/MS spectrum search tool for highly accurate and confident identification of endogenous peptides by combining two different fragmentation methods. Our approach takes advantage of the combination of two independent fragmentation methods (collision-induced dissociation and electron transfer dissociation). Their peptide spectral matching is carried out separately in both methods, and the final score is built as a combination of the two separate scores. We demonstrate that this approach is very effective in discriminating correct peptide identifications from false hits. We applied this approach to a spectral data set of neuropeptides extracted from mouse pituitary tumor cells. Compared to conventional MS-based identification, i.e., using a single fragmentation method, our approach significantly increased the peptide identification rate. It proved also highly effective for scanning spectra against a very large search space, enabling more accurate genome-wide searches and searches including multiple potential post-translational modifications.