Non-targeted Manner Research Articles

Nontargeted Identification of D-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS.

D-amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-L-amino acid residues. Amino acid residue isomerization greatly impacts the function of the resulting DAACP. However, because isomerization does not change the peptide's mass, this modification is difficult to detect by most mass spectrometry-based peptidomic approaches. Here we describe a method for the identification of DAACPs that can be used to systematically survey peptides extracted from a tissue sample in a nontargeted manner.

Identifying and Measuring Endogenous Peptides through Peptidomics.

Endogenous peptides, such as neuropeptides and peptide hormones, play important roles in intercellular communication, can provide information on physiology, and are potential sources of biomarkers. Mass spectrometry-based peptidomics methods are underutilized tools to identify and measure endogenous peptides in a relatively nontargeted manner. The purpose of this Viewpoint is to serve as a brief introduction to the field of peptidomics so that researchers interested in studying endogenous peptides are aware of this powerful approach and can consider its application.

New methods for trace analysis of gamma-irradiated pentaerythritol tetranitrate

High explosives (HEs) are used in a diverse range of applications in which they could be exposed to various radiation levels that may cause potential chemical changes. This study further evaluated pentaerythritol tetranitrate (PETN) that was previously aged with a low-level 2 kGy dose of gamma irradiation in order to understand chemical changes caused by irradiation. Both unirradiated PETN and gamma-irradiated PETN were analyzed using ultra high-pressure liquid chromatography coupled to quadrupole time of flight mass spectrometry (UHPLC-QTOF). The resulting data were processed in a non-targeted manner using Fisher's ratio analysis and multivariate curve resolution-alternating least squares (MCR-ALS) to aid in discovery and identification of the chemical changes brought about by irradiation without a priori knowledge. The application of using UHPLC-QTOF in combination with chemometric techniques for the analysis of irradiated samples has not previously been performed. Here we show how to use this method to provide chemical information that would otherwise not be discernible, such as the discovery of degradation of the various homologues of PETN. Major differences identified with radiolytic aging of the PETN sample included decomposition products that resulted from the degradation of the trigger linkage – the O–NO2 bonds – resulting in the formation of alcohol and aldehyde groups. Similar degradation was also observed in the PETN homologues as well as interconversion from one homologue to another.

Association of residual feed intake with intestinal microbiome and metabolome in laying period of ducks.

Residual feed intake (RFI) is a indicator to evaluate animal feed. This experiment was explored to study the relationship between intestinal microbiome and metabolome of ducks with different residual feed intake during laying period. A total of 300 Shaoxing ducks aged 42 weeks were randomly selected and fed a diet of 60 d. At the end of the trial, 20 samples were selected according to the phenotype of RFI and divided into two groups (HRFI and LRFI). The cecal microbiota composition was explored by 16S ribosomal RNA gene sequencing and rectal metabolomics uses liquid chromatography-mass spectrometry (LC-MS) to identify the composition of metabolites in a non-targeted manner. Results show feed intake and feed conversion ratio in the group HRFI were significantly higher than those in the group LRFI (p < 0.05). Chao1 indices were higher in the group LRFI than in the HRFI (p < 0.05), Shannon and Simpson indices were higher in the group LRFI than in the HRFI (p < 0.01). After linear discriminant analysis effect size (p < 0.05, LDA score > 3), Rikenellaceae, Rikenellaceae_RC9_gut_group, Lactobacillales and Ruminococcus_2, etc. were significantly enriched in the group LRFI at the genus level, while Prevotellaceae_NK3B31_group and Bacteria were significantly enriched in the group HRFI. After LC-MS analysis we found 338 metabolic difference products and 10 metabolic pathways, including the ABC transporter system, cysteine and methionine metabolism, arginine and proline metabolism, and vitamin B6 metabolism, were identified to be associated with the significantly differentially expressed between the groups LRFI and HRFI (p < 0.05). We hypothesize that the difference between ducks with different RFIs is mainly due to the fact that ducks with LRFI have more SCFAs-producing bacteria in their gut microorganisms, which regulate the RFI of animals. This process we found that Phascolarctobaterium and Anaerobiospirillum may provide energy for ABC transporter system by producing SCFAs, and regulate RFI to improve feed utilization efficiency. These results revealed the relationship between microbiome and metabonomics in laying ducks with different RFI, and provided theoretical basis for further study on the relationship between them.

Integrated Exposomics/Metabolomics for Rapid Exposure and Effect Analyses.

The totality of environmental exposures and lifestyle factors, commonly referred to as the exposome, is poorly understood. Measuring the myriad of chemicals that humans are exposed to is immensely challenging, and identifying disrupted metabolic pathways is even more complex. Here, we present a novel technological approach for the comprehensive, rapid, and integrated analysis of the endogenous human metabolome and the chemical exposome. By combining reverse-phase and hydrophilic interaction liquid chromatography (HILIC) and fast polarity-switching, molecules with highly diverse chemical structures can be analyzed in 15 min with a single analytical run as both column's effluents are combined before analysis. Standard reference materials and authentic standards were evaluated to critically benchmark performance. Highly sensitive median limits of detection (LODs) with 0.04 μM for >140 quantitatively assessed endogenous metabolites and 0.08 ng/mL for the >100 model xenobiotics and human estrogens in solvent were obtained. In matrix, the median LOD values were higher with 0.7 ng/mL (urine) and 0.5 ng/mL (plasma) for exogenous chemicals. To prove the dual-column approach's applicability, real-life urine samples from sub-Saharan Africa (high-exposure scenario) and Europe (low-exposure scenario) were assessed in a targeted and nontargeted manner. Our liquid chromatography high-resolution mass spectrometry (LC-HRMS) approach demonstrates the feasibility of quantitatively and simultaneously assessing the endogenous metabolome and the chemical exposome for the high-throughput measurement of environmental drivers of diseases.

Characterizing the Chemical Contaminants Diversity and Toxic Potential of Untreated Wastewater From a Drug Rehabilitation Hospital: Understanding Impact on Downstream Environment

This study characterizes a total of 21 wastewater samples collected from Al Amal hospital, and aims to determine if untreated hospital wastewater may impose a potentially detrimental impact on the downstream municipal biological wastewater treatment process. By means of solid phase extraction and liquid chromatography with tandem mass spectrometry (LC-MS/MS), chemical contaminants in these wastewater samples were determined in a non-targeted manner. In-silico characterization for the mutagenicity and reactive oxygen species (ROS) producing capabilities was performed by checking against database and literature. However, majority of the chemical contaminants have no prior information available and remain uncharacterized for both traits. Instead, in-vitro mutagenicity tests by means of Ames test showed that majority of the samples were non-mutagenic except for 5 samples that imposed mutagenic effect at high concentrations of &amp;gt;×10. In-vitro tests to determine for intracellular ROS production further showed that one of the mutagenic samples collected on Jun-22 positively induce ROS production and subsequently increased horizontal gene transfer via natural transformation. The findings in this study suggest that a specialty hospital like Al Amal does not frequently contribute mutagenic compounds and ROS to the wastewater streams, and in instances where it contributed positively, would require a high concentration to do so. Hence in general, wastewater streams from a specialty hospital like Al Amal may be unlikely to significantly perturb the downstream environment.

Generation of Gene Drive Mice for Invasive Pest Population Suppression.

Gene drives are genetic elements that are transmitted to greater than 50% of offspring and have potential for population modification or suppression. While gene drives are known to occur naturally, the recent emergence of CRISPR-Cas9 genome-editing technology has enabled generation of synthetic gene drives in a range of organisms including mosquitos, flies, and yeast. For example, studies in Anopheles mosquitos have demonstrated >95% transmission of CRISPR-engineered gene drive constructs, providing a possible strategy for malaria control. Recently published studies have also indicated that it may be possible to develop gene drive technology in invasive rodents such as mice. Here, we discuss the prospects for gene drive development in mice, including synthetic "homing drive" and X-shredder strategies as well as modifications of the naturally occurring t haplotype. We also provide detailed protocols for generation of gene drive mice through incorporation of plasmid-based transgenes in a targeted and non-targeted manner. Importantly, these protocols can be used for generating transgenic mice for any project that requires insertion of kilobase-scale transgenes such as knock-in of fluorescent reporters, gene swaps, overexpression/ectopic expression studies, and conditional "floxed" alleles.

MassBase: A large-scaled depository of mass spectrometry datasets for metabolome analysis.

Depository of low-molecular-weight compounds or metabolites detected in various organisms in a non-targeted manner is indispensable for metabolomics research. Due to the diverse chemical compounds, various mass spectrometry (MS) setups with state-of-the-art technologies have been used. Over the past two decades, we have analyzed various biological samples by using gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, or capillary electrophoresis-mass spectrometry, and archived the datasets in the depository MassBase (http://webs2.kazusa.or.jp/massbase/). As the format of MS datasets depends on the MS setup used, we converted each raw binary dataset of the mass chromatogram to text file format, and thereafter, information of the chromatograph peak was extracted in the text file from the converted file. In total, the depository comprises 46,493 datasets, of which 38,750 belong to the plant species and 7,743 are authentic or mixed chemicals as well as other sources (microorganisms, animals, and foods), as on August 1, 2020. All files in the depository can be downloaded in bulk from the website. Mass chromatograms of 90 plant species obtained by LC-Fourier transform ion cyclotron resonance MS or Orbitrap MS, which detect the ionized molecules with high accuracy allowing speculation of chemical compositions, were converted to text files by the software PowerGet, and the chemical annotation of each peak was added. The processed datasets were deposited in the annotation database KomicMarket2 (http://webs2.kazusa.or.jp/km2/). The archives provide fundamental resources for comparative metabolomics and functional genomics, which may result in deeper understanding of living organisms.

Nontargeted Identification of Plasma Proteins O-, N-, and S-Transmethylated by O-Methyl Organophosphates

Organophosphates (OPs) are used worldwide as pesticides. However, acute and chronic exposure to OPs can cause serious adverse health effects. The mechanism of delayed OP toxicity is thought to involve off-target inhibition of serine proteases, although the precise molecular details remain unclear owing to the lack of an analytical method for global detection of protein targets of OPs. Here, we report the development of a mass spectrometry method to identify OP-adducted proteins from complex mixtures in a nontargeted manner. Human plasma was incubated with the OP dichlorvos that was 50% isotopically labeled and 50% unlabeled. Proteins and protein adducts were extracted, digested, and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to detect "twin ions" of peptides that were covalently modified by a chemical reaction with dichlorvos. The LC-MS/MS data were processed by a blended data analytics software (Xenophile) to detect the amino acid residue sites of proteins that were covalently modified by exposure to OPs. We discovered that OPs can transmethylate the N, S, and O side chains of His, Cys, Glu, Asp, and Lys residues. For model systems, such transmethylation reactions were confirmed by LC-MS, nuclear magnetic resonance (NMR), and rationalized using electronic structure calculations. Methylation of the ubiquitous antioxidant glutathione by dichlorvos can decrease the reducing/oxidizing equilibrium of glutathione in liver extracts, which has been implicated in diseases and pathological conditions associated with delayed OP toxicity.

Chemical Composition, Spatial Homogeneity, and Growth of Indoor Surface Films

Organic films on indoor surfaces are ubiquitous, but details about their composition and growth over timescales less than a month are not fully understood. To address these gaps in understanding, organic film samples in an apartment unit were collected over the course of 17 days using passive samplers and analyzed in a non-targeted manner using direct analysis in real-time mass spectrometry (DART-MS). Overall, the chemical composition observed across various locations within the apartment are very similar. Mass spectra also show clear evidence for the growth of semi-volatile compounds from natural sources and consumer products, such as carboxylic acids and plasticizers. Certain compounds show evidence for equilibration, mostly consistent with surface partitioning models based on octanol-air partition coefficients (Koa). Compounds which have higher molecular weight or larger Koa values tend to equilibrate later, leading to an overall shift in the composition of the film as a function of collection time. Growth rates of film thickness are at least 0.05 nm/day based on a limited number of individually calibrated ions.

Development and Application of a High-Precision Algorithm for Nontarget Identification of Organohalogens Based on Ultrahigh-Resolution Mass Spectrometry.

Brominated and/or chlorinated organic compounds (referred to as organohalogens) are frequently detected in natural and engineered environments. However, ultrahigh-resolution mass spectrometry (UHR-MS)-based nontargeted identification of organohalogens remains challenging because of the coexistence of a vast number of halogenated and nonhalogenated organic molecules. In this study, a new algorithm, namely, the NOMDBP code, was developed to simultaneously identify organohalogens and non-organohalogens from the UHR-MS spectra of natural and engineered waters. In addition to isotopic patterns, for the first time, three optional filter rules [i.e., selection for minimum nonoxygen heteroatoms, inspection of the presence of newly formed halogenated disinfection byproducts (Xn-DBPs), and of their precursors] were incorporated into our code, which can accurately identify DBP-associated peaks and further elucidate Xn-DBP generation and transformation mechanisms. The formula assignment ratio against 2815 previously reported organohalogens, and their 11,583 isotopologues exceeded 97%. Application of our algorithm to disinfected natural organic matter indicated that oxygen-containing Xn-DBP species accounted for a majority of the Xn-DBPs. Furthermore, brominated Xn-DBPs (Br-DBPs) were characterized by a higher degree of unsaturation compared to chlorinated Xn-DBPs. In addition to electrophilic substitution and electrophilic addition reactions, the decomposition/transformation pathway was found to be another important mechanism in Br-DBP formation. The results of this study highlight the superior potential of our code for the efficient detection of yet unknown organohalogens (including organohalogens bearing nonoxygen heteroatoms) in a nontargeted manner and for the identification of their generation mechanism occurring during the disinfection process.

4022 Recruiting hidden and sensitive populations: methods for recruitment of pregnant women who regularly use cannabinoids

OBJECTIVES/GOALS: Prenatal cannabinoid use is increasing and more studies are needed to describe the neurodevelopmental impact on the fetus. However, pregnant cannabinoid users are a “hidden population,” which makes identification of these individuals for research difficult. Our study will employ three methods of recruitment and evaluate the success of each method. METHODS/STUDY POPULATION: We will recruit a total of 40 women in the third trimester of pregnancy who regularly use cannabinoid products thought to contain tetrahydrocannabinol (THC) and/or cannabidiol (CBD) throughout their pregnancies, and 20 control pregnant women who do not use those products. The purpose of this study is to evaluate the effects of prenatal cannabinoid use on the neurodevelopment of their offspring over the first year of life. We will employ three recruitment methods. First, targeted recruitment will occur in two university-based obstetrical clinics, where the obstetrician will present the study material and contact information. Second, we will utilize social media advertisements targeted to a specific demographic of Facebook users. Finally, we will employ the traditional method of distributing flyers in a non-targeted manner. We will track methods of recruitment success and gather information from the mothers on their preferences for recruitment approaches. RESULTS/ANTICIPATED RESULTS: Recruitment will start in January 2020 and continue for several months. We anticipate that the targeted method will yield the highest number of participants, and participants with the best fit for the inclusion criteria. However, it is possible that those women will be deterred by fear of having their drug use status revealed to their care providers, even though all research activity will occur independently from clinic visits and will not be transmitted to the electronic health record. The inclusion of a control group will also help foster “anonymity” for participants. The social media method has the potential for the greatest reach, but we expect many of these potential participants will fail to meet inclusion/exclusion criteria, as this is not as targeted as the first method. We anticipate a similar issue with the flyer-based approach. DISCUSSION/SIGNIFICANCE OF IMPACT: Optimizing recruitment of hidden and sensitive populations is crucial for clinical and translational research. Our goal is to identify strategies that can lead to best practices for engagement of those populations. Our conclusions could be applied in recruitment of sensitive populations for other clinical and translational research projects.

Source-related smart suspect screening in the aqueous environment: search for tire-derived persistent and mobile trace organic contaminants in surface waters

A variant of suspect screening by liquid chromatography–high-resolution mass spectrometry (LC-HRMS) is proposed in this study: Samples of a potential source of contamination and of an environmental sample close to this source are first analyzed in a non-targeted manner to select source-related suspects and to identify them. The suspect list compiled from such an exercise is then applied to LC-HRMS data of environmental samples to ascribe and to identify persistent and mobile contaminants in the water cycle that may originate from the source under study. This approach was applied to tire crumb rubber (source) and road dust (close to source); by comparison of the two data sets, 88% of the features detected in tire leachate could be excluded. Of the 48 suspects remaining, a total of 41 could be tentatively identified as either related to hexamethoxymethyl melamine or cyclic amines, benzothiazoles, or glycols. Subsequently, environmental samples were searched for these suspects: 85% were determined in an urban creek after a combined sewer overflow and 67% in the influent of a municipal wastewater treatment plant (WWTP). These exceptionally high rates of positive findings prove that this source-related smart suspect screening effectively directs the effort of selecting and identifying unknown contaminants to those related to the source of interest. The WWTP effluent and the urban creek during dry weather also showed the presence of numerous contaminants that may stem from tire and road wear particles (TRWP) in road runoff. Contribution from other sources, however, cannot be ruled out.Graphical abstract

Non-Targeted Mass Isotopolome Analysis Using Stable Isotope Patterns to Identify Metabolic Changes.

Gas chromatography coupled with mass spectrometry can provide an extensive overview of the metabolic state of a biological system. Analysis of raw mass spectrometry data requires powerful data processing software to generate interpretable results. Here we describe a data processing workflow to generate metabolite levels, mass isotopomer distribution, similarity and variability analysis of metabolites in a nontargeted manner, using stable isotope labeling. Using our data analysis software, no bioinformatic or programming background is needed to generate results from raw mass spectrometry data.

PROMIS: Global Analysis of PROtein-Metabolite Interactions.

Small molecules are not only intermediates of metabolism, but also play important roles in signaling and in controlling cellular metabolism, growth, and development. Although a few systematic studies have been conducted, the true extent of protein-small molecule interactions in biological systems remains unknown. PROtein-metabolite interactions using size separation (PROMIS) is a method for studying protein-small molecule interactions in a non-targeted, proteome- and metabolome-wide manner. This approach uses size-exclusion chromatography followed by proteomics and metabolomics liquid chromatography-mass spectrometry analysis of the collected fractions. Assuming that small molecules bound to proteins would co-fractionate together, we found numerous small molecules co-eluting with proteins, strongly suggesting the formation of stable complexes. Using PROMIS, we identified known small molecule-protein complexes, such as between enzymes and cofactors, and also found novel interactions. © 2019 The Authors. Basic Protocol 1: Preparation of native cell lysate from plant material Support Protocol: Bradford assay to determine protein concentration Basic Protocol 2: Separation of molecular complexes using size-exclusion chromatography Basic Protocol 3: Simultaneous extraction of proteins and metabolites using single-step extraction protocol Basic Protocol 4: Metabolomics analysis Basic Protocol 5: Proteomics analysis.

The Use of TAT Peptide-Functionalized Graphene as a Highly Nuclear-Targeting Carrier System for Suppression of Choroidal Melanoma.

Tumorous metastasis is a difficult challenge to resolve for researchers and for clinicians. Targeted delivery of antitumor drugs towards tumor cells’ nuclei can be a practical approach to resolving this issue. This work describes an efficient nuclear-targeting delivery system prepared from trans-activating transcriptional activator (TAT) peptide-functionalized graphene nanocarriers. The TAT peptide, originally observed in a human immunodeficiency virus 1 (HIV-1), was incorporated with graphene via an edge-functionalized ball-milling method developed by the author’s research group. High tumor-targeting capability of the resulting nanocarrier was realized by the strong affinity between TAT and the nuclei of cancer cells, along with the enhanced permeability and retention (EPR) effect of two-dimensional graphene nanosheets. Subsequently, a common antitumor drug, mitomycin C (MMC), was covalently linked to the TAT-functionalized graphene (TG) to form a nuclear-targeted nanodrug MMC-TG. The presence of nanomaterials inside the nuclei of ocular choroidal melanoma (OCM-1) cells was shown using transmission electron microscopy (TEM) and confocal laser scanning microscopy. In vitro results from a Transwell co-culture system showed that most of the MMC-TG nanodrugs were delivered in a targeted manner to the tumorous OCM-1 cells, while a very small amount of MMC-TG was delivered in a non-targeted manner to normal human retinal pigment epithelial (ARPE-19) cells. TEM results further confirmed that apoptosis of OCM-1 cells was started from the lysis of nuclear substances, followed by the disappearance of nuclear membrane and cytoplasm. This suggests that the as-synthesized MMC-TG is a promising nuclear-target nanodrugfor resolution of tumorous metastasis issues at the headstream.

Mass Spectrometry-Based Tissue Imaging: The Next Frontier in Clinical Diagnostics?

The diagnosis of tissue samples traditionally has been performed by anatomic pathologists using a combination of cellular staining and light microscopy. With these techniques, pathologists can characterize various tissue features including cell morphology, structure, and composition to subsequently confirm whether a disease process is present. Although the histopathologic “gold-standard” methods are invaluable for routine tissue diagnosis, the results can be subjective, owing to a combination of factors such as variability in staining quality, nature of the sample, and human interpretation, and inconclusive for diseases that present indistinguishable histologic features. There is a need for new technologies that can be used as complementary tools in pathology for objective tissue analysis and disease diagnosis. Mass spectrometry (MS)7 imaging has been heralded as an upcoming advance in tissue analysis. The ability of MS to rapidly identify a variety of biomolecules present in a sample is highly attractive to the clinical laboratory. Indeed, MS coupled to chromatographic separation techniques is currently used to detect and/or quantify small molecules such as pharmacological agents and hormones in blood and urine. The advent of MS techniques that allow direct tissue analysis, including MALDI-MS and secondary ion MS, has allowed laboratories to extend the use of MS beyond biofluids into tissue samples. Using MALDI MS, for example, thin tissue sections can be analyzed in a nontargeted manner for the abundance and spatial distribution of biomolecules. As such, MALDI-MS imaging is being increasingly applied in clinical research, especially in the context of cancer diagnostics based on tissue proteomic and lipidomic signatures. The potential of MS in revolutionizing tissue analysis and diagnosis has driven several advances to accelerate its feasibility and utility in the clinical setting. The development of ambient ionization MS (AIMS), for example, has brought MS-based tissue imaging even closer to routine clinical use. Unlike MALDI and …

Non-targeted Identification of D-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS.

D-Amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-L-amino acid residues. Amino acid residue isomerization greatly impacts the function of the resulting DAACP. However, because isomerization does not change the peptide's mass, this modification is difficult to detect by most mass spectrometry-based peptidomic approaches. Here we describe a method for the identification of DAACPs that can be used to systematically survey peptides extracted from a tissue sample in a non-targeted manner.

Characterization of smokeless powders using multiplexed collision-induced dissociation mass spectrometry and chemometric procedures

This work demonstrates a non-targeted mass spectrometry approach for identification of organic compounds in smokeless powders. Unburned powders were removed from various commercial ammunitions of different brand, primer composition, caliber, and age. The unburned powders and corresponding fired residues were analyzed by liquid chromatography–atmospheric pressure chemical ionization-time-of-flight mass spectrometry (LC–APCI-TOFMS). Multiplexed collision-induced dissociation was performed at increasing collision potentials resulting in successive fragmentation that provided structural information for compound identification in a non-targeted manner. Nine compounds were identified in the powders, including akardite II, ethyl centralite, diphenylamine, N-nitrosodiphenylamine, and dibutyl phthalate.Multivariate statistical procedures were performed to first investigate association and discrimination of the unburned powders. Principal components analysis (PCA) of the chemical profiles suggested nine distinct groups of powders, according to the dominant organic compounds present. The clusters formed in hierarchical cluster analysis (HCA) were mostly in agreement with PCA groupings although HCA provided a metric to quantify the similarity. Finally, association of the fired residue to the corresponding unburned powder was possible although the success was highly dependent on the composition of the unburned powder and the extent of compound depletion as a result of firing.

A d-Amino Acid-Containing Neuropeptide Discovery Funnel.

A receptor binding class of d-amino acid-containing peptides (DAACPs) is formed in animals from an enzymatically mediated post-translational modification of ribosomally translated all-l-amino acid peptides. Although this modification can be required for biological actions, detecting it is challenging because DAACPs have the same mass as their all-l-amino acid counterparts. We developed a suite of mass spectrometry (MS) protocols for the nontargeted discovery of DAACPs and validated their effectiveness using neurons from Aplysia californica. The approach involves the following three steps, with each confirming and refining the hits found in the prior step. The first step is screening for peptides resistant to digestion by aminopeptidase M. The second verifies the presence of a chiral amino acid via acid hydrolysis in deuterium chloride, labeling with Marfey’s reagent, and liquid chromatography–mass spectrometry to determine the chirality of each amino acid. The third involves synthesizing the putative DAACPs and comparing them to the endogenous standards. Advantages of the method, the d-amino acid-containing neuropeptide discovery funnel, are that it is capable of detecting the d-form of any common chiral amino acid, and the first two steps do not require peptide standards. Using these protocols, we report that two peptides from the Aplysia achatin-like neuropeptide precursor exist as GdYFD and SdYADSKDEESNAALSDFA. Interestingly, GdYFD was bioactive in the Aplysia feeding and locomotor circuits but SdYADSKDEESNAALSDFA was not. The discovery funnel provides an effective means to characterize DAACPs in the nervous systems of animals in a nontargeted manner.