Field Of Proteomics Research Articles

Graph representation learning for structural proteomics.

The field of structural proteomics, which is focused on studying the structure–function relationship of proteins and protein complexes, is experiencing rapid growth. Since the early 2000s, structural databases such as the Protein Data Bank are storing increasing amounts of protein structural data, in addition to modeled structures becoming increasingly available. This, combined with the recent advances in graph-based machine-learning models, enables the use of protein structural data in predictive models, with the goal of creating tools that will advance our understanding of protein function. Similar to using graph learning tools to molecular graphs, which currently undergo rapid development, there is also an increasing trend in using graph learning approaches on protein structures. In this short review paper, we survey studies that use graph learning techniques on proteins, and examine their successes and shortcomings, while also discussing future directions.

Evaluating the Performance of 193 nm Ultraviolet Photodissociation for Tandem Mass Tag Labeled Peptides

Despite the successful application of tandem mass tags (TMT) for peptide quantitation, missing reporter ions in higher energy collisional dissociation (HCD) spectra remains a challenge for consistent quantitation, especially for peptides with labile post-translational modifications. Ultraviolet photodissociation (UVPD) is an alternative ion activation method shown to provide superior coverage for sequencing of peptides and intact proteins. Here, we optimized and evaluated 193 nm UVPD for the characterization of TMT-labeled model peptides, HeLa proteome, and N-glycopeptides from model proteins. UVPD yielded the same TMT reporter ions as HCD, at m/z 126–131. Additionally, UVPD produced a wide range of fragments that yielded more complete characterization of glycopeptides and less frequent missing TMT reporter ion channels, whereas HCD yielded a strong tradeoff between characterization and quantitation of TMT-labeled glycopeptides. However, the lower fragmentation efficiency of UVPD yielded fewer peptide identifications than HCD. Overall, 193 nm UVPD is a valuable tool that provides an alternative to HCD for the quantitation of large and highly modified peptides with labile PTMs. Continued development of instrumentation specific to UVPD will yield greater fragmentation efficiency and fulfil the potential of UVPD to be an all-in-one spectrum ion activation method for broad use in the field of proteomics.

AccuCor2: isotope natural abundance correction for dual-isotope tracer experiments

Stable isotope labeling techniques have been widely applied in the field of metabolomics and proteomics. Before the measured mass spectral data can be used for quantitative analysis, it must be accurately corrected for isotope natural abundance and tracer isotopic impurity. Despite the increasing popularity of dual-isotope tracing strategy such as 13C-15N or 13C-2H, there are no accurate tools for correcting isotope natural abundance for such experiments in a resolution-dependent manner. Here, we present AccuCor2 as an R-based tool to perform the correction for 13C-15N or 13C-2H labeling experiments. Our method uses a newly designed algorithm to construct the correction matrices that link labeling pattern and measured mass fractions, then use non-negative least-squares to solve the labeling patterns. Our results show that the dual-isotope experiments often require a mass resolution that is high enough to resolve 13C and 15N or 13C and 2H. Otherwise, the labeling pattern is not solvable. However, this mass resolution may not be sufficiently high to resolve other non-tracer elements such as oxygen or sulfur from the tracer elements. Therefore, we design AccuCor2 to perform the correction based on the actual mass resolution of the measurements. Using both simulated and experimental data, we show that AccuCor2 performs accurate and resolution-dependent correction for dual-isotope tracer data.The authors developed AccuCor2 as the first resolution-dependent method for accurate isotope natural abundance correction of experimental data generated from dual-isotope tracers. They show that such correction requires a minimum resolution to resolve tracer isotopologues. AccuCor2 showed improved accuracy more than previously developed tools, which assume infinite resolution of the instrument.

La inflamación y su relación con el cáncer

Inflammation and cancer have been two of
 the most studied topics in Biomedical Sciences during the
 last decades. Scientific and technological advances
 in the fields of genomics and proteomics have made
 it is possible to establish with precision a great variety
 of immunological, cellular and genetic mechanisms
 that allow inflammation to be directly associated with
 cancer. Of the many studies derived from this topic,
 the one written by Hanahan and Weinberg in 2000
 stands out, since it describes the biology of cancer
 in six proper characteristics or hallmarks of tumor
 development, which are nothing more than a series of
 responses and biological interactions of tumor cells in
 their initiation, development and progression phases,
 which are favored by elements directly or indirectly
 associated with inflammation. A decade later, the
 same authors have added more hallmarks to tumor
 biology and have dug into the role of the inflammatory
 response as a constant element that allows tumor
 development and invasion, since the inflammatory
 response is modulated and organized to promote key
 elements for tumor survival. The importance of the
 inflammatory infiltrate is key to understanding the
 development of neoplasms. This review will describe
 the main inflammatory cellular elements associated
 and modified by cancer cells to evade their elimination
 by the host, and some mechanisms to facilitate their
 progression.

Molecular Proteomics and Signalling of Human Platelets in Health and Disease

Platelets are small anucleate blood cells that play vital roles in haemostasis and thrombosis, besides other physiological and pathophysiological processes. These roles are tightly regulated by a complex network of signalling pathways. Mass spectrometry-based proteomic techniques are contributing not only to the identification and quantification of new platelet proteins, but also reveal post-translational modifications of these molecules, such as acetylation, glycosylation and phosphorylation. Moreover, target proteomic analysis of platelets can provide molecular biomarkers for genetic aberrations with established or non-established links to platelet dysfunctions. In this report, we review 67 reports regarding platelet proteomic analysis and signalling on a molecular base. Collectively, these provide detailed insight into the: (i) technical developments and limitations of the assessment of platelet (sub)proteomes; (ii) molecular protein changes upon ageing of platelets; (iii) complexity of platelet signalling pathways and functions in response to collagen, rhodocytin, thrombin, thromboxane A2 and ADP; (iv) proteomic effects of endothelial-derived mediators such as prostacyclin and the anti-platelet drug aspirin; and (v) molecular protein changes in platelets from patients with congenital disorders or cardiovascular disease. However, sample sizes are still low and the roles of differentially expressed proteins are often unknown. Based on the practical and technical possibilities and limitations, we provide a perspective for further improvements of the platelet proteomic field.

Recent Advances about the Applications of Click Reaction in Chemical Proteomics.

Despite significant advances in biological and analytical approaches, a comprehensive portrait of the proteome and its dynamic interactions and modifications remains a challenging goal. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to elucidate protein composition, distribution, and relevant physiological and pharmacological functions. Click chemistry focuses on the development of new combinatorial chemical methods for carbon heteroatom bond (C-X-C) synthesis, which have been utilized extensively in the field of chemical proteomics. Click reactions have various advantages including high yield, harmless by-products, and simple reaction conditions, upon which the molecular diversity can be easily and effectively obtained. This paper reviews the application of click chemistry in proteomics from four aspects: (1) activity-based protein profiling, (2) enzyme-inhibitors screening, (3) protein labeling and modifications, and (4) hybrid monolithic column in proteomic analysis.

Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic Standard.

Over the past decade, the data-independent acquisition mode has gained popularity for broad coverage of complex proteomes by LC-MS/MS and quantification of low-abundance proteins. However, there is no consensus in the literature on the best data acquisition parameters and processing tools to use for this specific application. Here, we present the most comprehensive comparison of DIA workflows on Orbitrap instruments published so far in the field of proteomics. Using a standard human 48 proteins mixture (UPS1-Sigma) at 8 different concentrations in an E.coli proteome background, we tested 36 workflows including 4 different DIA window acquisition schemes and 6 different software tools (DIA-NN, DIA-Umpire, OpenSWATH, ScaffoldDIA, Skyline, and Spectronaut) with or without the use of a DDA spectral library. On the basis of the number of proteins identified, quantification linearity and reproducibility, as well as sensitivity and specificity in 28 pairwise comparisons of different UPS1 concentrations, we summarize the major considerations and propose guidelines for choosing the DIA workflow best suited for LC-MS/MS proteomic analyses. Our 96 DIA raw files and software outputs have been deposited on ProteomeXchange for testing or developing new DIA processing tools.

Precision medicine and inflammatory bowel diseases: concept, strategies, future

With the advent of modern cellular and genomic technologies, we have become participants in the integration of such areas as personalized, predictive, preventive, and precision medicine (referred to as 4P-medicine), into practical healthcare. In replace of the classic methods of diagnosis and treatment of diseases comes medicine, which makes it possible to predict (anticipate) the disease, and a personalized approach to each patient, taking into account their genetic, biochemical and physiological uniqueness. Precision medicine aims to improve the quality of medical care by opening up an individual approach to the patient and covers a wide range of areas, including drug therapy, genetics, and cause-and-effect relationships in order to make the right decisions based on evidence. 4P-medicine combines knowledge in the field of proteomics, metabolomics, genomics, bioinformatics with classical approaches of anatomy, therapy, laboratory and instrumental diagnostics as well as public health. The purpose of this review is to analyze and summarize the information available to date and to present examples of the application of modern approaches of medicine into clinical practice by diving into the example of inflammatory bowel diseases (IBD). The search for literature containing scientific information about relevant studies was conducted in the PubMed and Google Scholar systems with the use of the following keywords: precision medicine, 4P medicine, inflammatory bowel diseases. Despite significant progress in medicine in general, there is still a long way to go before implementing the principles of precision medicine in the field of IBD, since many clinicians continue to treat patients with IBD symptomatically. However, the use of specific biomarkers and new treatment strategies as described in the review, can significantly accelerate this path and contribute to the improvement of diagnostic and therapeutic approaches.

Current advances in metabolomic studies on non-motor psychiatric manifestations of Parkinson's disease (Review).

Life expectancy has increased worldwide and, along with it, a greater prevalence of age-dependent disorders, chronic illnesses and comorbidities can be observed. In 2019, in both Europe and the Americas, dementias ranked 3rd among the top 10 causes of death. Parkinson's disease (PD) is the second most frequent type of neurodegenerative disease. In the last decades, globally, the number of people suffering from PD has more than doubled to over 6 million. Of all the neurological disorders, PD increased with the fastest rate. This troubling trend highlights the stringent need for accurate diagnostic biomarkers, especially in the early stages of the disease and to evaluate treatment response. To gain a broad and complex understanding of the recent advances in the ‘-omics’ research fields, electronic databases such as PubMed, Google Academic, and Science Direct were searched for publications regarding metabolomic studies on PD to identify specific biomarkers for PD, and especially PD with associated psychiatric symptomatology. Discoveries in the fields of metagenomics, transcriptomics and proteomics, may lead to an improved comprehension of the metabolic pathways involved in disease etiology and progression and contribute to the discovery of novel therapeutic targets for effective treatment options.

Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade

ABSTRACT Introduction Pioneering technologies such as proteomics have helped fuel the biotechnology and pharmaceutical industry with the discovery of novel targets and an intricate understanding of the activity of therapeutics and their various activities in vitro and in vivo. The field of proteomics is undergoing an inflection point, where new sensitive technologies are allowing intricate biological pathways to be better understood, and novel biochemical tools are pivoting us into a new era of chemical proteomics and biomarker discovery. In this review, we describe these areas of innovation, and discuss where the fields are headed in terms of fueling biotechnological and pharmacological research and discuss current gaps in the proteomic technology landscape. Areas Covered Single cell sequencing and single molecule sequencing. Chemoproteomics. Biological matrices and clinical samples including biomarkers. Computational tools including instrument control software, data analysis. Expert Opinion Proteomics will likely remain a key technology in the coming decade, but will have to evolve with respect to type and granularity of data, cost and throughput of data generation as well as integration with other technologies to fulfill its promise in drug discovery.

Integration of Segmented Ion Fractionation and Differential Ion Mobility on a Q-Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer.

High-field asymmetric waveform ion mobility spectrometry (FAIMS) has gained popularity in the proteomics field for its capability to improve mass spectrometry sensitivity and to decrease peptide co-fragmentation. The recent implementation of FAIMS on Tribrid Orbitrap instruments enhanced proteome coverage and increased the precision of quantitative measurements. However, the FAIMS interface has not been available on older generation Orbitrap mass spectrometers such as the Q-Exactive. Here, we report the integration of the FAIMS Pro device with embedded electrical and gas connections to a Q-Exactive HF mass spectrometer. Proteomic experiments performed on HeLa tryptic digests with the modified mass spectrometer improved signal to noise and reduced interfering ions, resulting in an increase of 42% in peptide identification. FAIMS was also combined with segmented ion fractionation where 100 m/z windows were obtained in turn to further increase the depth of proteome analysis by reducing the proportion of chimeric MS/MS spectra from 50 to 27%. We also demonstrate the application of FAIMS to improve quantitative measurements when using isobaric peptide labeling. FAIMS experiments performed on a two-proteome model revealed that FAIMS Pro provided a 65% improvement in quantification accuracy compared to conventional LC-MS/MS experiments.

Challenges and Strategies in the Development of Radiation Biodosimetry Tests for Patient Management.

The public health and medical response to a radiological or nuclear incident requires the capability to sort, assess, treat, triage and ultimately discharge, as well as to refer or transport people to their next step in medical care. The Public Health Emergency Medical Countermeasures Enterprise (PHEMCE), directed by the U.S. Department of Health and Human Services (HHS), facilitates a comprehensive, multi-agency effort to develop and deploy radiation biodosimetry tests. Within HHS, discovery and development of biodosimetry tests includes the National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH), the Office of the Assistant Secretary of Preparedness and Response (ASPR), Biomedical Advanced Research and Development Authority (BARDA), and the Food and Drug Administration (FDA) as primary partners in this endeavor. The study of radiation biodosimetry has advanced significantly, with expansion into the fields of cytogenetics, genomics, proteomics, metabolomics, lipidomics and transcriptomics. In addition, expansion of traditional cytogenetic assessment methods using automated platforms, and development of laboratory surge capacity networks have helped to advance biodefense preparedness. This article describes various programs and coordinating efforts between NIAID, BARDA and FDA in the development of radiation biodosimetry approaches to respond to radiological and nuclear threats.

Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data using HIT-MAP

Spatial proteomics has the potential to significantly advance our understanding of biology, physiology and medicine. Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) is a powerful tool in the spatial proteomics field, enabling direct detection and registration of protein abundance and distribution across tissues. MALDI-MSI preserves spatial distribution and histology allowing unbiased analysis of complex, heterogeneous tissues. However, MALDI-MSI faces the challenge of simultaneous peptide quantification and identification. To overcome this, we develop and validate HIT-MAP (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets and generate customisable spatial distribution maps. HIT-MAP will be a valuable resource for the spatial proteomics community for analysing newly generated and retrospective datasets, enabling robust peptide and protein annotation and visualisation in a wide array of normal and disease contexts.

Overview on capillary electrophoresis with mass spectrometry: Application in peptide analysis and proteomics

The pharmaceutical industry and most particularly the biopharmaceutical industry are demanding advancements in analytical techniques. The field of proteomics and peptide mapping needs sensitive analysis and sophisticated instrumentation, which needs hyphenated analytical techniques to be explored. In addition to effective detection and characterization, Due to efficient and selective separation, predominant focus has been drawn to capillary electrophoresis/mass spectrometry (CE/MS) compared to widely used techniques such as slab-gel electrophoresis (SGE), liquid chromatography (LC) and capillary electrophoresis (CE) Several significant advances in CE/MS instrumentation and software have made CE/MS a competitive tool in the last decade to solve a wide variety of analytical and biopharmaceutical problems. This analysis discusses the technological aspects of CE / MS interfaces, analytical separation modes, MS analyzer, recent CE / MS approaches and applications specific to biopharmaceutical. Applications using some of the more common electrophoretic separation modes, such as conventional electrophoresis of the capillary zone (CZE) and capillary isoelectric focusing (CIEF), have been highlighted. The peptide analysis also includes recent studies on capillary electro-chromatography (CEC) / MS and CE-MS applications.

Novel Strategies to Address the Challenges in Top-Down Proteomics.

Top-down mass spectrometry (MS)-based proteomics is a powerful technology for comprehensively characterizing proteoforms to decipher post-translational modifications (PTMs) together with genetic variations and alternative splicing isoforms toward a proteome-wide understanding of protein functions. In the past decade, top-down proteomics has experienced rapid growth benefiting from groundbreaking technological advances, which have begun to reveal the potential of top-down proteomics for understanding basic biological functions, unraveling disease mechanisms, and discovering new biomarkers. However, many challenges remain to be comprehensively addressed. In this Account & Perspective, we discuss the major challenges currently facing the top-down proteomics field, particularly in protein solubility, proteome dynamic range, proteome complexity, data analysis, proteoform-function relationship, and analytical throughput for precision medicine. We specifically review the major technology developments addressing these challenges with an emphasis on our research group's efforts, including the development of top-down MS-compatible surfactants for protein solubilization, functionalized nanoparticles for the enrichment of low-abundance proteoforms, strategies for multidimensional chromatography separation of proteins, and a new comprehensive user-friendly software package for top-down proteomics. We have also made efforts to connect proteoforms with biological functions and provide our visions on what the future holds for top-down proteomics.

Performance of nanoflow liquid chromatography using core-shell particles: A comparison study

Due to its unique structure, core-shell material has presented significantly improved chromatographic performance in comparison with conventional totally porous material. This has been well demonstrated in the analytical column format, e.g. 4.6 mm i.d. columns. In the proteomics field, there is always a demand for high resolution microseparation tools. In order to explore core-shell material's potential in proteomics-oriented microseparations, we investigated chromatographic performance of core-shell material in a nanoLC format, as well as its resolving power for protein digests. The results show core-shell nanoLC columns have similar van Deemter curves to the totally porous particle-packed nanoLC columns. For 100 µm i.d. capillary columns, the core-shell material does not have significantly better dynamics. However, both core-shell and totally porous particle-packed nanoLC columns have shown high efficiencies: plate heights of ~11 µm, equivalent to 90000 plates per meter, have been achieved with 5 µm particles. Using a 60 cm long core-shell nanoLC column, 72000 plates were realized in an isocratic separation of neutral compounds. For a 15 cm long nanoLC column, a maximum peak capacity of 220 has been achieved in a 5 hour gradient separation of protein digests, indicating the high resolving power of core-shell nanoLC columns. With a standard HeLa cell lysate as the sample, 2546 proteins were identified by using the core-shell nanoLC column, while 2916 proteins were identified by using the totally porous particle-packed nanoLC column. Comparing the two sets of proteomics data, it was found that 1830 proteins were identified by both columns, while 1086 and 716 proteins were uniquely identified by using totally porous and core-shell particle-packed nanoLC columns, respectively, suggesting their complementarity in nanoLC-MS based proteomics.

A Compendium on Hypertension: New Advances and Future Impact.

A Compendium on Hypertension: New Advances and Future Impact.

GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis.

Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MALDI-TOF is a combined technology in mass spectrometry with many applications in characterizing biological samples from different sources, such as the identification of cancer biomarkers, the detection of food frauds, the identification of doping substances in athletes’ fluids, and so on. The massive quantity of data, in the form of mass spectra, are often biased and altered by different sources of noise. Therefore, extracting the most relevant features that characterize the samples is often challenging and requires combining several computational methods. Here, we present GeenaR, a novel web tool that provides a complete workflow for pre-processing, analyzing, visualizing, and comparing MALDI-TOF mass spectra. GeenaR is user-friendly, provides many different functionalities for the analysis of the mass spectra, and supports reproducible research since it produces a human-readable report that contains function parameters, results, and the code used for processing the mass spectra. First, we illustrate the features available in GeenaR. Then, we describe its internal structure. Finally, we prove its capabilities in analyzing oncological datasets by presenting two case studies related to ovarian cancer and colorectal cancer. GeenaR is available at http://proteomics.hsanmartino.it/geenar/.

Stoichiometric Thiol Redox Proteomics for Quantifying Cellular Responses to Perturbations.

Post-translational modifications regulate the structure and function of proteins that can result in changes to the activity of different pathways. These include modifications altering the redox state of thiol groups on protein cysteine residues, which are sensitive to oxidative environments. While mass spectrometry has advanced the identification of protein thiol modifications and expanded our knowledge of redox-sensitive pathways, the quantitative aspect of this technique is critical for the field of redox proteomics. In this review, we describe how mass spectrometry-based redox proteomics has enabled researchers to accurately quantify the stoichiometry of reversible oxidative modifications on specific cysteine residues of proteins. We will describe advancements in the methodology that allow for the absolute quantitation of thiol modifications, as well as recent reports that have implemented this approach. We will also highlight the significance and application of such measurements and why they are informative for the field of redox biology.

Microbiome in Death and Beyond: Current Vistas and Future Trends

Forensic medicine has, for a long time, been relying on biochemical, anthropologic, and histopathologic evidences in solving various investigations. However, depending on the method used, lengthy sample processing time, scanty sample, and less sensitivity and accuracy pervade these procedures. Accordingly, newer arenas such as the thanatomicrobiome have come forward to aid in its quandaries; furthermore, the parallel advances in genomic and proteomic techniques have complemented and are still emerging to be used in forensic experiments and investigations. Postmortem interval (PMI) is one of the most important aspects of medico-legal investigations. The current trend in PMI estimation is toward genomic analyses of autopsy samples. Similarly, determination of cause of death, although a domain of medical sciences, is being targeted as the next level of forensic casework. With the current trend in laboratory sciences moving to the discovery of newer disease-specific markers for diagnostic and prognostic purposes, the same is being explored for the determination of the cause of death by using techniques such as Real-Time PCR, DNA micro-array, to Next-Gen Sequencing. Establishing an individual’s biological profile has been done using medicolegal methods and anthropology as well as bar-bodies/Davidson bodies (gender determination); and in cases where the determination of age/gender is a challenge using morphological characteristics; the recent advances in the field of genomics and proteomics have played a significant role, e.g., use of mitochondrial DNA in age estimation and in maternity disputes. The major hurdle forensic medical research faces is the fact that most of the studies are conducted in animal models, which are often difficult to mimic in human and real-time scenarios. Additionally, the high accuracy required in criminal investigations to be used in a court of law as evidence has prevented these results to come out of the labs and be used to the optimum. The current review aims at giving a comprehensive and critical account of the various molecular biology techniques including “thanatogenomics,” currently being utilized in the veritable fields of forensic medicine.