Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring.

Existing mass spectrometric assays used for sensitive and specific measurements of target proteins across multiple samples, such as selected/multiple reaction monitoring (SRM/MRM) or parallel reaction monitoring (PRM), are peptide-based methods for bottom-up proteomics. Here, we describe an approach based on the principle of PRM for the measurement of intact proteoforms by targeted top-down proteomics, termed proteoform reaction monitoring (PfRM). We explore the ability of our method to circumvent traditional limitations of top-down proteomics, such as sensitivity and reproducibility. We also introduce a new software program, Proteoform Finder (part of ProSight Native), specifically designed for the easy analysis of PfRM data. PfRM was initially benchmarked by quantifying three standard proteins. The linearity of the assay was shown over almost 3 orders of magnitude in the femtomole range, with limits of detection and quantification in the low femtomolar range. We later applied our multiplexed PfRM assay to complex samples to quantify biomarker candidates in peripheral blood mononuclear cells (PBMCs) from liver-transplanted patients, suggesting their possible translational applications. These results demonstrate that PfRM has the potential to contribute to the accurate quantification of protein biomarkers for diagnostic purposes and to improve our understanding of disease etiology at the proteoform level.

Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire.

Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS, a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multiparametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We applied Ig-MS to plasma from subjects with severe and mild COVID-19 and immunized subjects after two vaccine doses, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, that could use other antigens of interest to gauge immune responses to vaccination, pathogens, or autoimmune disorders.

Peroxisome proliferator-activated receptor delta-PPARδ agonist (L-165041) enhances bovine embryo survival and post vitrification viability.

The effect of L-165041 (PPARδ-agonist) on decreasing apoptosis and intracellular lipid content was assessed in fresh and vitrified-warmed in vitro -produced bovine embryos. It was hypothesised that the addition of L-165041 to the culture medium enhances development and cryopreservation. Oocytes were allocated to one of two treatments: control-standard culture medium, or L-165041 added to the medium on day1 with no media change. Ultrastructure, cleavage, and blastocyst rates were evaluated in fresh, and in post-vitrification cultured embryos by optical and electronic microscopy. A subset of fresh embryos were fixed for TUNEL assay and for Sudan-Black-B histochemical staining. Vitrified-warmed embryos were assessed using MALDI-MS technique. Cleavage and blastocyst rates (control 49.4±5.2, L-165041 51.8±4.3) were not influenced by L-165041. The proportion of inner cell mass cells (ICM) was higher in fresh embryos, and the rate of total and ICM apoptosis was lower in L-165041. In warmed-embryos, total and ICM apoptosis was lower in L-165041. The overall hatching rate was higher in L-165041 (66.62±2.83% vs 53.19±2.90%). There was less lipid accumulation in fresh L-165041-embryos. In conclusion, the use of L-165041 is recommended to improve the viability of in vitro -derived bovine embryos.

Bulk IgG glycosylation predicts COVID-19 severity and vaccine antibody response.

Although vaccination efforts have expanded, there are still gaps in our understanding surrounding the immune response to SARS-CoV-2. Measuring IgG Fc glycosylation provides insight into an infected individual's inflammatory state, among other functions. We set out to interrogate bulk IgG glycosylation changes from SARS-CoV-2 infection and vaccination, using plasma from mild or hospitalized COVID-19 patients, and from vaccinated individuals. Inflammatory glycans are elevated in hospitalized COVID-19 patients and increase over time, while mild patients have anti-inflammatory glycans that increase over time, including increased sialic acid correlating with RBD antibody levels. Vaccinated individuals with low RBD antibody levels and low neutralization have the same IgG glycan traits as hospitalized COVID-19 patients. In addition, a small vaccinated cohort reveals a decrease in inflammatory glycans associated with peak IgG concentrations and neutralization. This report characterizes the bulk IgG glycome associated with COVID-19 severity and vaccine responsiveness and can help guide future studies into SARS-CoV-2 protective immunity.

The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells.

Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of ~30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma from human blood and bone marrow. The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. We demonstrate the potential for clinical application, by interrogating the BPA in the context of liver transplantation and identifying cell and proteoform signatures that distinguish normal graft function from acute rejection and other causes of graft dysfunction.

Effects of paternal diet and antioxidant addition to the semen extender on bovine semen characteristics and on the phenotype of the resulting embryo.

The aim of this study was to examine the effects of long-term dietary supplementation of young Nellore bulls with rumen-protected polyunsaturated fatty acids (PUFAs) and of the inclusion of catalase in the semen extender on semen quality, in vitro sperm fertilizing ability, and intracytoplasmic lipid content in the resulting embryos. Twelve Nellore bulls were supplemented with rumen-protected PUFAs or with a basal diet from 14 to 24 months of age. The semen was collected at the end of supplementation. For cryopreservation, the ejaculate was divided into two equal volumes and catalase was added to the extender in one of the fractions. Thus, the experimental design consisted of a 2 × 2 factorial scheme with two diets (control and PUFA) and two extenders (Cat+ and Cat-). Total motility and the percentage of rapid cells in fresh semen were negatively affected by dietary supplementation with PUFAs (P < 0.05), but these effects did not persist after freezing. The frozen/thawed semen of animals fed PUFAs exhibited an increase in the percentages of damaged plasma and acrosomal membranes, as well as an increase in the proportion of lipids ions at m/z 578 and m/z 757 detected by MALDI-MS. Nevertheless, there was no effect of the treatments on in vitro embryo development. However, embryos derived from bulls supplemented with PUFAs exhibited higher lipid accumulation compared to control (P < 0.05). In conclusion, PUFA supplementation promoted worsening of semen quality without affecting the in vitro sperm fertilizing ability; however, the paternal diet affected the intracytoplasmic lipid content in the resulting embryos.

Next-generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire.

Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS , a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multi-parametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We apply Ig-MS to plasma from subjects with severe & mild COVID-19, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, with compatibility to any recombinant antigen to gauge our immune responses to vaccination, pathogens, or autoimmune disorders.

Proteomics of Select Neglected Tropical Diseases.

Technological advances in mass spectrometry have enabled the extensive identification, characterization, and quantification of proteins in any biological system. In disease processes proteins are often altered in response to external stimuli; therefore, proteomics, the large-scale study of proteins and their functions, represents an invaluable tool for understanding the molecular basis of disease. This review highlights the use of mass spectrometry-based proteomics to study the pathogenesis, etiology, and pathology of several neglected tropical diseases (NTDs), a diverse group of disabling diseases primarily associated with poverty in tropical and subtropical regions of the world. While numerous NTDs have been the subject of proteomic studies, this review focuses on Buruli ulcer, dengue, leishmaniasis, and snakebite envenoming. The proteomic studies highlighted provide substantial information on the pathogenic mechanisms driving these diseases; they also identify molecular targets for drug discovery and development and uncover promising biomarkers that can assist in early diagnosis.

Peptide profile and angiotensin-converting enzyme inhibitory activity of Prato cheese with salt reduction and Lactobacillus helveticus as an adjunct culture.

Among strategies to improve the health-related aspects of dairy products, great prominence has been given to salt reduction and the use of adjunct cultures that can favor the release of bioactive peptides during cheese ripening. This study aimed to evaluate the effect of the salt reduction, the addition of Lactobacillus helveticus LH-B02 and the ripening time of Prato cheese on the casein hydrolysis profile by capillary electrophoresis, peptide profile by mass spectrometry, and antihypertensive potential evaluated in vitro through the inhibitory activity of the angiotensin-converting enzyme (ACE). Both the salt reduction and the addition of adjunct culture favored the accumulation of the bioactive peptide ß-CN (f193-209) (m/z 1881). The adjunct culture led to a higher ACE inhibitory activity during the ripening of Prato cheese, thus proving to be an effective strategy for the development of potentially bioactive cheese.

High protein yogurt with addition of Lactobacillus helveticus: Peptide profile and angiotensin-converting enzyme ACE-inhibitory activity.

In order to evaluate differences in the peptide profile and bioactive potential in dairy products, by increasing the protein content and using proteolytic bacteria strain to enable the release of bioactive peptides, a high-protein yogurt with adjunct culture was developed. The effect of protein content, the addition of Lactobacillus helveticus LH-B02, and storage time were evaluated. The qualitative analysis of peptide profile was performed using a mass spectrometry approach (MALDI-ToF-MS), and the potential bioactivity evaluated by ACE inhibition activity. Protein content did not affect the peptide profile in yogurts, and the addition of Lactobacillus helveticus LH-B02 favored the formation of peptides recognized as bioactive, such as αS1-CN f(24-32) and ß-CN f(193-209). Increased protein content and adjunct culture addition increased the ACE inhibitory activity. The combination of both factors had no additional effect on the bioactive potential of yogurts.

Comparative Proteomic Analysis of Murine Cutaneous Lesions Induced by Leishmania amazonensis or Leishmania major.

Cutaneous leishmaniasisis is the most common clinical form of leishmaniasis and one of the most relevant neglected diseases. It is known that the progress of the disease is species specific and the host's immune response plays an important role in its outcome. However, the pathways that lead to parasite clearance or survival remain unknown. In this work, skin tissue from mice experimentally infected with L. amazonensis, one of the causative agents of cutaneous leishmaniasis in the Amazon region, L. major, another causative agent of cutaneous leishmaniasis in Africa, the Middle East, China, and India, or lipopolysaccharides from Escherichia coli as an inflammation model were investigated using label-free proteomics to unveil Leishmania-specific protein alterations. Proteomics is a powerful tool to investigate host-pathogen relationships to address biological questions. In this work, proteins from mice skin biopsies were identified and quantified using nano-LC coupled with tandem mass spectrometry analyses. Integrated Proteomics Pipeline was used for peptide/protein identification and quantification. Western blot was used for validation of protein quantification by mass spectrometry, and protein pathways were predicted using Ingenuity Pathway Analysis. In this proteomics study, several proteins were pointed out as hypothetical targets to guide future studies on Leishmania-specific modulation of proteins in the host. We identified hundreds of exclusively modulated proteins after Leishmania spp. infection and 17 proteins that were differentially modulated in the host after L. amazonensis or L. major infection.

Tandem Mass Tag Proteomic Analysis of in Vitro and in Vivo Models of Cutaneous Leishmaniasis Reveals Parasite-Specific and Nonspecific Modulation of Proteins in the Host.

Cutaneous leishmaniasis, the most common form of leishmaniasis, is endemic in several regions of the world, and if not treated properly, it can cause disfiguring scars on the skin. Leishmania spp. infection causes an inflammatory response in its host, and it modulates the host metabolism differently depending on the Leishmania species. Since Leishmania spp. has begun to develop resistance against current therapies, we believe efforts to identify new possibilities for treatment are critical for future control of the disease. Proteomics approaches such as isobaric labeling yield accurate relative quantification of protein abundances and, when combined with chemometrics/statistical analysis, provide robust information about protein modulation across biological conditions. Using a mass spectrometry-based proteomics approach and tandem mass tag labeling, we have investigated protein modulation in murine macrophages (in vitro model) and skin biopsies after exposure to Leishmania spp. (in vivo murine model). Infections induced by L. amazonensis (endemic in the New World) and L. major (endemic in the Old World) were compared to an inflammation model to search for Leishmania-specific and nonspecific protein modulation in the host. After protein extracts obtained from in vitro and in vivo experiments were digested, the resulting peptides were labeled with isobaric tags and analyzed by liquid chromatography-MS (LC-MS). Several proteins that were found to be changed upon infection with Leishmania spp. provide interesting candidates for further investigation into disease mechanism and development of possible immunotherapies.

Peptide profile of Camembert-type cheese: Effect of heat treatment and adjunct culture Lactobacillus rhamnosus GG.

Several factors might impact the proteolysis during cheese manufacture and ripening and, therefore, the release of bioactive peptides. These factors include the heat treatment of the milk, the type of starter and secondary culture used and the ripening time. Thus, the objective of this study was to evaluate the effect of the milk heat treatment and the use of adjunct culture in the development of the peptide profile of Camembert-type cheese during ripening. The cheeses were made from raw and heat-treated milk, with and without the addition of Lactobacillus rhamnosus GG. The results obtained by mass spectrometry (MALDI ToF/MS) and analyzed by chemometrics (PLS-DA) revealed a complex hydrolysis profile of the caseins with 103 peaks found, of which 70 peptides were identified and 15 presented bioactive potential. The potential bioactive peptides important for the separation of cheeses were all derived from ß-casein. The heat treatment of the milk, the addition of the adjunct culture and the ripening time affected the peptide profile of the cheeses. At the beginning of ripening the cheeses presented a very similar peptide profile, which differed over time, and this differentiation is clearer for cheeses obtained from raw milk.

Label-Free Proteomic Analysis Reveals Parasite-Specific Protein Alterations in Macrophages Following Leishmania amazonensis, Leishmania major, or Leishmania infantum Infection.

Leishmania is an obligate intracellular parasite known to modulate the host cell to survive and proliferate. However, the complexity of host-parasite interactions remains unclear. Also, the outcome of the disease has been recognized to be species-specific and dependent on the host's immune responses. Proteomics has emerged as a powerful tool to investigate the host-pathogen interface, allowing us to deepen our knowledge about infectious diseases. Quantification of the relative amount of proteins in a sample can be achieved using label-free proteomics, and for the first time, we have used it to quantify Leishmania-specific protein alterations in macrophages. Protein extracts were obtained and digested, and peptides were identified and quantified using nano-LC coupled with tandem mass spectrometry analyses. Protein expression was validated by Western blot analysis. Integrated Proteomics Pipeline was used for peptide/protein identification and for quantification and data processing. Ingenuity Pathway Analysis was used for network analysis. In this work, we investigated how this intracellular parasite modulates protein expression on a host macrophage by comparing three different Leishmania species- L. amazonensis, one of the causative agents of cutaneous disease in the Amazon region; L. major, another causative agent of cutaneous leishmaniasis in Africa, the Middle East, China, and India; L. infantum, the causative agent of visceral leishmaniasis affecting humans and dogs in Latin America-and lipopolysaccharide stimulated macrophages as an in vitro inflammation model. Our results revealed that Leishmania infection downregulates apoptosis pathways while upregulating the activation of phagocytes/leukocytes and lipid accumulation.

Molecular Signatures of High-Grade Cervical Lesions.

Cervical cancer is the fourth most common neoplasia in women and the infection with human papilloma virus (HPV) is its necessary cause. Screening methods, currently based on cytology and HPV DNA tests, display low specificity/sensitivity, reducing the efficacy of cervical cancer screening programs. Herein, molecular signatures of cervical cytologic specimens revealed by liquid chromatography-mass spectrometry (LC-MS), were tested in their ability to provide a metabolomic screening for cervical cancer. These molecules were tested whether they could clinically differentiate insignificant HPV infections from precancerous lesions. For that, high-grade squamous intraepithelial lesions (HSIL)-related metabolites were compared to those of no cervical lesions in women with and without HPV infection. Samples were collected from women diagnosed with normal cervix (N = 40) and from those detected with HSIL from cytology and colposcopy (N = 40). Liquid-based cytology diagnosis, DNA HPV-detection test, and LC-MS analysis were carried out for all the samples. The same sample, in a customized collection medium, could be used for all the diagnostic techniques employed here. The metabolomic profile of cervical cancer provided by LC-MS was found to indicate unique molecular signatures for HSIL, being two ceramides and a sphingosine metabolite. These molecules occurred independently of women's HPV status and could be related to the pre-neoplastic phenotype. Statistical models based on such findings could correctly discriminate and classify HSIL and no cervical lesion women. The results showcase the potential of LC-MS as an emerging technology for clinical use in cervical cancer screening, although further validation with a larger sample set is still necessary.

Proteomic approaches for drug discovery against tegumentary leishmaniasis.

Tegumentary leishmaniases (TL) comprise various clinical forms, in which current therapeutic treatments lack in safety and efficacy. Recently the parasite is developing resistance mechanisms against anti leishmanial drugs startling the scientific community to recruit efforts to search for novel therapeutics. Proteomics hold promises for the treatment of leishmaniasis and investigation of parasite-host interaction since these set of methodological tools have provided a wealth of protein expression data on several Leishmania species. Firstly this review puts together the current treatment and challenges to fight tegumentary leishmaniasis. In addition, the 2 dimensional gel electrophoresis and mass spectrometry techniques in protein identification and characterization are described and discussed in the context of proteomics regarding Leishmania studies. In this review, we selected literature content on TL causative agents. Important proteomic findings related to differentiation proteome (promastigote and amastigote forms), Leishmania-macrophage interaction proteome and secreted and soluble proteins including molecules involved in parasite resistance and potential drug targets are examined and discussed. We also highlight open questions regarding drug research that can be addressed with proteomics approaches.

Murine cutaneous leishmaniasis investigated by MALDI mass spectrometry imaging.

Imaging mass spectrometry (IMS) is recognized as a powerful tool to investigate the spatial distribution of untargeted or targeted molecules of a wide variety of samples including tissue sections. Leishmania is a protozoan parasite that causes different clinical manifestations in mammalian hosts. Leishmaniasis is a major public health risk in different continents and represents one of the most important neglected diseases. Cutaneous lesions from mice experimentally infected with Leishmania spp. were investigated by matrix-assisted laser desorption ionization MS using the SCiLS Lab software for statistical analysis. Being applied to cutaneous leishmaniasis (CL) for the first time, MALDI-IMS was used to search for peptides and low molecular weight proteins (2-10 kDa) as candidates for potential biomarkers. Footpad sections of Balb/c mice infected with (i) Leishmania amazonensis or (ii) Leishmania major were imaged. The comparison between healthy and infected skin highlighted a set of twelve possible biomarker proteins for L. amazonenis and four proteins for L. major. Further characterization of these proteins could reveal how these proteins act in pathology progression and confirm their values as biomarkers.

Lipidomic alterations of in vitro macrophage infection by L. infantum and L. amazonensis.

Particular lipid profiles have been found in two different protozoa of the Leishmania genus. Leishmania infantum, a visceral leishmaniasis causative agent and Leishmania amazonensis, a cutaneous leishmaniasis, reveal distinctive lipid contents of phosphatidylethanolamine and phosphatidylserine plasmalogens, sphingolipids, phosphatidylinositols, phosphatidylcholine, and phosphatidylethanolamine, which have been shown to be related to species, life-cycle of the parasite, and macrophage infection. L. infantum displayed a higher content of phosphatidylethanolamine plasmalogens than L. amazonensis, which may help to differentiate their unique clinical manifestations. Phosphatidylserines plasmalogens are also found to be an important lipid class for the intracellular form of the parasite. Our findings also reveal lipid classes that may be involved in visceralization pathways and parasite differentiation.