Revealing the diversity of endogenous peptides and parent proteins in human colostrum and mature milk through peptidomics analysis

Endogenous peptides and their parent proteins are important nutritional components with diverse biological functions. The objective of this study was to analyze and compare endogenous peptides and parent proteins found in human colostrum (HC) and human mature milk (HM) using a 4D label-free technique. In total, 5162 and 940 endogenous peptides derived from 258 parent proteins were identified in human milk by database (DB) search and de novo, respectively. Among these peptides, 2446 differentially expressed endogenous peptides with various bioactivities were identified. The Gene Ontology analysis unveiled the cellular components, biological processes, and molecular functions associated with these parent proteins. Metabolic pathway analysis suggested that neutrophil extracellular trap formation had the greatest significance with 24 parent proteins. These findings will offer a fresh perspective on the development of infant formula powder, highlighting the potential for incorporating these changes to enhance its nutritional composition and benefits.

A Seedling Growth Inhibition Assay to Measure Phytocytokine Activity

The study of immunomodulatory peptides, both of exogenous and endogenous origin, attracted increasing attention over the last years. Numerous methods are widely used to study the sensitivity of plants to peptide elicitation, ranging from measuring early to late induced responses. Seedling growth inhibition is a prominent and easy-to-measure output induced by prolonged peptide treatment. Here, we describe a robust Arabidopsis thaliana seedling growth inhibition experiment that can be used to measure the direct growth-inhibitory effect of peptides, exemplified by RAPID ALKALINIZATION FACTOR 23 (RALF23) treatment. We also show how the assay can be used to assess the modulatory effect of peptide co-treatment on microbe-associated molecular pattern (MAMP)-triggered seedling growth inhibition, exemplified by GOLVEN 2 (GLV2)`s effect on flagellin (flg22)-induced seedling growth inhibition.

The Strategy for Peptidomic LC-MS/MS Data Analysis: The Case of Urinary Peptidome Study

The study of urinary peptidome is an important area of research, which concerns the characterization of endogenous peptides, as well as the identification of biomarkers for a wide range of socially significant diseases. First of all, this relates to renal and genitourinary pathologies and/or pathologies associated with proteinuria, such as kidney diseases, bladder, prostate and ovarian cancers, diabetic nephropathy, and pre-eclampsia. Unlike proteins, peptides do not require proteolytic hydrolysis, can be analyzed in their native form and can provide certain information about occurring (patho)physiological processes. Mass spectrometry (MS)-based approaches are the most unbiased and sensitive instruments with high multiplexing capacity and provided most of the current information about endogenous urine peptides. However, despite the large number of urine peptidomic studies, there are certain issues related to the insufficient comparability of their results due to the lack of consistent approaches to their interpretation. Also the development of a custom project-specific protein library for endogenous peptides search and identification is another important point that should be noted in the context of high-throughput peptidomic analysis. Here we propose the custom-specific urinary protein database and the grouping of endogenous urinary peptides with overlapping sequences as useful tools, which can facilitate the acquisition and analysis of LC-MS peptidomic data, as well as the comparison of results of different studies, which should facilitate their more efficient further application.

Exploring novel ANGICon-EIPs through ameliorated peptidomics techniques: Can deep learning strategies as a core breakthrough in peptide structure and function prediction?

Dairy-derived angiotensin-I-converting enzyme inhibitory peptides (ANGICon-EIPs) have been regarded as a relatively safe supplementary diet-therapy strategy for individuals with hypertension, and short-chain peptides may have more relevant antihypertensive benefits due to their direct intestinal absorption. Our previous explorations have confirmed that endogenous goat milk short-chain peptides are also an essential source of ANGICon-EIPs. Nonetheless, there are limited explorations on endogenous ANGICon-EIPs owing to the limitations of the extraction and enrichment of endogenous peptides, currently. This review outlined ameliorated pre-treatment strategies, data acquisition methods, and tools for the prediction of peptide structure and function, aiming to provide creative ideas for discovering novel ANGICon-EIPs. Currently, deep learning-based peptide structure and function prediction algorithms have achieved significant advancements. The convolutional neural network (CNN) and peptide sequence-based multi-label deep learning approach for determining the multi-functionalities of bioactive peptides (MLBP) can predict multiple peptide functions with absolute true value and accuracy of 0.699 and 0.708, respectively. Utilizing peptide sequence input, torsion angles, and inter-residue distance to train neural networks, APPTEST predicted the average backbone root mean square deviation (RMSD) value of peptide (5-40 aa) structures as low as 1.96 Å. Overall, with the exploration of more neural network architectures, deep learning could be considered a critical research tool to reduce the cost and improve the efficiency of identifying novel endogenous ANGICon-EIPs.

Discovery of Missing Methylation Sites on Endogenous Peptides of Human Cell Lines

Methylation of proteins has considerable impacts on physiological processes including signal transduction, DNA damage repair, transcriptional regulation, gene activation, and inhibition of gene expression. However, the traditional proteomics-based approach suffers from limited identification rates of these critical methylation sites on endogenous peptides. In this work, a peptidomics-based workflow was established to discover and characterize the global methylome of endogenous peptides in human cells. The reliability of our strategy was validated by methyl-SILAC labeling, resulting in 83% true-positive identifications in the HeLa cell line. We applied this approach to seven human cell lines, and 700 methylated forms on 646 putative methylation sites were identified in total, with over 61% of the methylation sites being newly identified. This study provides a complementary strategy for a traditional proteomics-based approach that enables identification of missing methylation sites and creates a first methylome draft of endogenous peptides of human cell lines, offering a valuable resource for in-depth studies of biological functions of methylated endogenous peptides.

Magnetic mesoporous silica of loading copper metal ions for enrichment and LC-MS/MS analysis of salivary endogenous peptides

Peptidomics research is of great significance for discovering potential biomarkers and monitoring human diseases. As a kind of common clinical biofluid, saliva known for its noninvasive collection and easy accessibility has been widely used in peptidomics research. In this article, we combined immobilized metal ions affinity chromotography (IMAC) with mesoporous material and proposed the copper ion doped magnetic mesoporous silica material (denoted as Fe₃O₄@mSiO₂-Cu²⁺) which had a large surface area of 221 m² g^-1 and pore volume of 0.20 cm³ g^-1. By immobilizing copper ions onto the mesopore walls, the standard peptide Angiotensin II could be identified in an extremely low concentration of 0.1 fmol μl^-1 and in a mass ratio of 1:500 (Angiotensin II:BSA, m/m), which indicated significant sensitivity and a great size-exclusive ability. In addition, the introduction of polydopamine (PDA) made Fe₃O₄@mSiO₂-Cu²⁺ more hydrophilic and biocompatible which could improve the profiling of endogenous peptides in bio-sample. Finally, 131 endogenous peptides were identified in human saliva after enrichment with Fe₃O₄@mSiO₂-Cu²⁺. Therefore, Fe₃O₄@mSiO₂-Cu²⁺ nanoparticles provided a promising candidate protocol for biomarker discovery.

Peptidomic Workflow Applied to Cerebrospinal Fluid Analysis

Proteo-peptidomic profiling of biofluids is used to identify disease biomarkers and to study molecular mechanisms of pathology development. Previously, we studied changes in cerebrospinal fluid (CSF) and blood plasma associated with Guillain-Barre syndrome (GBS)-a rare and severe disorder of the peripheral nervous system with an unknown etiology. Here, we describe the workflow for the analysis of endogenous peptides from CSF. The procedure covers sample preparation, liquid chromatography-mass spectrometry (LC-MS) analysis, and bioinformatics analysis and allows identification of more than 1100 peptides from 181 protein groups in ~3 h from a single CSF sample derived from non-neurological, non-oncological patients.

Use of the tau protein-to-peptide ratio in CSF to improve diagnostic classification of Alzheimer's disease

Cerebrospinal fluid (CSF) tau and phospho-tau are well established biomarkers of Alzheimer's disease. While these measures are conventionally referred to as 'total tau' (T-tau) and 'phospho-tau' (P-tau), several truncated and modified tau forms exist that may relay additional diagnostic information. We evaluated the diagnostic performance of an endogenous tau peptide in CSF, tau 175-190, in the phosphorylated and non-phosphorylated state. A liquid chromatography-mass spectrometry (LC-MS) method was established to measure these peptides in CSF and was used to analyze two independent clinical cohorts; the first cohort included patients with Alzheimer's disease (AD, n = 15), Parkinson's disease (PD, n = 15), progressive supranuclear palsy (PSP, n = 15), and healthy controls (n = 15), the second cohort included AD patients (n = 16), and healthy controls (n = 24). In both cohorts T-tau and P-tau concentrations were determined by immunoassay. While tau 175-190 and P-tau 175-190 did not differentiate the study groups, the separation of AD and controls by T-tau (area under the ROC Curve (AUC) = 95%) and P-tau (AUC = 92%) was improved when normalizing the ELISA measurements to the concentrations of the endogenous peptides: T-tau/tau 175-190 (AUC = 100%), P-tau/P-tau 175-190 (AUC = 95%). The separation between patients and controls by T-tau (AUC = 88%) and P-tau (AUC = 82%) was similarly improved in the second cohort by taking the ratios of T-tau/tau 175-190 (AUC = 97%) and P-tau/P-tau 175-190 (AUC = 98%). In conclusion, our results suggest that the performance of the AD biomarkers T-tau and P-tau could be improved by normalizing their measurements to the endogenous peptides tau 175-190 and P-tau 175-190, possibly because these endogenous tau peptides serve to normalize for physiological, and disease-independent, secretion of tau from neurons to the extracellular space and the CSF. Finally, the observations made here add to the general applicability of mass spectrometry as a tool for rapid identification and accurate quantification of biomarker candidates.

Toward an efficient workflow for the analysis of the human milk peptidome

There is a growing interest for investigating endogenous peptides from human biofluids which may provide yet unknown functional benefits or provide an early indication of disease states as potential biomarkers. A major technical bottleneck in the investigation of endogenous peptides from body fluids, e.g., serum, urine, saliva, and milk, is that each of these fluids seems to require unique workflows for peptide extraction and analysis. Thus, protocols optimized for serum cannot be directly translated to milk. One biofluid that is readily available, but which has not been extensively explored, is human milk, whose analysis could contribute to our understanding of the immune development of the newborn infant. Due to the occurrence of highly abundant lipids, proteins, and saccharides, milk peptidomics requires dedicated sample preparation steps. The aim of this study was to develop a time and cost-efficient workflow for the analysis of the human milk peptidome, for which we compared peptide extraction methodologies and peptide fragmentation methods. A method using strong acid protein precipitation and analysis by collision-induced dissociation fragmentation was found to be superior to all other test methods, allowing us qualitative and quantitative detection of about 4000 endogenous human milk peptides in a total analysis time of just 18 h.

Mass spectrometry-based peptidome profiling of human serous ovarian cancer tissues

BACKGROUND

Bioactive peptides existing in vivo have been considered as an important class of natural medicines for the treatment of diseases. Peptidome analysis of tissues and biofluids had provided important information about the differentially expressed bioactive peptides in vivo.

METHODS

Here, we analyzed the peptidome of serous ovarian cancer tissue samples and normal ovarian epithelial tissue samples by mass spectrometry and further investigated the possible bioactive peptides that were differentially expressed.

RESULTS

We identified 634 differentially expressed peptides, 508 of these peptides were highly abundant in serous ovarian cancer tissues, a result consistent with higher protease activity in ovarian cancer patients. The difference in preferred cleavage sites between the serous ovarian cancer tissues and normal ovarian epithelium indicated the characteristic peptidome of ovarian cancer and the nature of cancer-associated protease activity. Interestingly, KEGG pathway analysis of the peptide precursors indicated that the differentially regulated pathways in ovarian cancer are highly consistent with the pathways discovered in other cancers. Besides, we found that a proportion of the differentially expressed peptides are similar to the known immune-regulatory peptides and anti-bacterial peptides. Then we further investigated the function of the two down-regulated peptides in ovarian cancer cells and found that peptide P1DS significantly inhibited the invasion and migration of OVCAR3 and SKOV3 ovarian cancer cells.

CONCLUSIONS

Our results are the first to identify the differentially expressed peptides between the serous ovarian cancer tissue and the normal ovarian epithelium. Our results indicate that bioactive peptides involved in tumorigenesis are existed in vivo.

Isolation of Endogenous Peptides from Cultured Cell Conditioned Media for Mass Spectrometry

Media conditioned by cultured cells represent an excellent source rich in endogenous peptides. Unbiased mass spectrometric analysis of the constituent peptides provides an opportunity to look into proteolytic events such as bioactive peptide processing, membrane protein ectodomain shedding, or even regulated intramembrane proteolysis. If conducted on a large scale, peptidomics has the potential to pinpoint primary cleavage sites. Here a method is described for isolating peptides from cultured cell conditioned media before mass spectrometry analysis.

Mass Spectrometric Identification of Endogenous Peptides

Peptidomics is an emerging field focused in the analysis of endogenous peptides. Naturally occurring peptides are often endogenously produced protein fragments. Cleavage of precursor proteins by proteases generates peptides that may gain specialized functions not ascribed to their precursors, and which could reflect the state of a cell under certain physiological conditions or pathological processes.Since peptides are found in complex matrices (e.g., serum, tear, urine, cerebrospinal fluid), they need to be isolated from the matrix and concentrated before they can be analyzed on mass spectrometry. This chapter describes methods for sample preparation prior to mass spectrometry analysis. In addition, different peptide fragmentation techniques are described which are complementary when analyzing naturally occurring peptides by liquid chromatography coupled online to tandem mass spectrometry.

Antimicrobial activity and mechanism of PDC213, an endogenous peptide from human milk

Human milk has always been considered an ideal source of elemental nutrients to both preterm and full term infants in order to optimally develop the infant's tissues and organs. Recently, hundreds of endogenous milk peptides were identified in human milk. These peptides exhibited angiotensin-converting enzyme inhibition, immunomodulation, or antimicrobial activity. Here, we report the antimicrobial activity and mechanism of a novel type of human antimicrobial peptide (AMP), termed PDC213 (peptide derived from β-Casein 213-226 aa). PDC213 is an endogenous peptide and is present at higher levels in preterm milk than in full term milk. The inhibitory concentration curve and disk diffusion tests showed that PDC213 had obvious antimicrobial against S. aureus and Y. enterocolitica, the common nosocomial pathogens in neonatal intensive care units (NICUs). Fluorescent dye methods, electron microscopy experiments and DNA-binding activity assays further indicated that PDC213 can permeabilize bacterial membranes and cell walls rather than bind intracellular DNA to kill bacteria. Together, our results suggest that PDC213 is a novel type of AMP that warrants further investigation.

Selective extraction of endogenous peptides from human serum with magnetic mesoporous carbon composites

Highly sensitive and selective enrichment of endogenous peptides or proteins from complex bio-system takes a significant important place to the proteomic. In this work, a unique Fe₃O₄@2SiO₂@mSiO₂-C nanomaterial was synthesized, contributing to the separation and enrichment of low concentration peptides from complex mixture. The highly ordered mesoporous carbon structure render the nanospheres with unique properties of strongly connected pore channels, strong hydrophobic properties, high specific surface area (254.90m²/g), uniform pore size (3.61nm). Which made it a promising candidates for the efficient enrichment of peptides through hydrophobic-hydrophobic interaction with low detection limit (0.2fmol), superb size-exclusion of high molecular weight proteins, highly selectivity for BSA digest (molar ratio of BSA tryptic digests/BSA, 1:400), ideal peptides recovery (about 87.5%), wonderful repeatability (RSD less than 25%). Moreover, the as-prepared Fe₃O₄@2SiO₂@mSiO₂-C nanoparticles were successfully enriched 2198 endogenous peptides from human serum, which fully indicated that the mesoporous carbon nanoparticles was a promising candidate for isolating proteins or peptides from complex biologicals.

AGHLDDLPGALSAL: A hemoglobin fragment potentially competing with albumin to bind transition metal ions

Protein degradation leads to the formation of endogenous peptides, the biological activity of which is most often unknown. The peptide AGHLDDLPGALSAL, recently isolated from mouse brain homogenates, has been recognized as a fragment of the α-chain of hemoglobin. AGHLDDLPGALSAL has the ability of inhibiting the peripheral hyperalgesic inflammatory responses through the indirect activation of the μ-opioid receptors. A peculiarity of AGHLDDLPGALSAL is the presence, at its N-terminus of a strong binding site for divalent transition metal ions, similar to that characterizing the human albumin and called "ATCUN motif". The consequential metal binding ability of AGHLDDLPGALSAL can be connected to its biological activity. For this reason, we decided to investigate the coordination properties of AGHLDDLPGALSAL towards Cu(II), Ni(II) and Zn(II) ions, reported here for the first time. The results confirm that AGHLDDLPGALSAL is a strong ligand for those metals: it can even compete with albumin under suitable conditions. In vitro assays on the inhibition of Cu(II) toxicity towards different cell lines confirmed that the binding ability of AGHLDDLPGALSAL can imply relevant biological consequences.