☆ 4.3 Review

Peptidomics

NATURE REVIEWS METHODS PRIMERS (2023)

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Review Spectroscopy

Recent advances in mass spectrometry analysis of neuropeptides

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Summary: Neuropeptides have become the focus of many recent research studies due to their involvement in numerous biochemical pathways. Traditional analytical methods are limited in terms of global investigations, leading researchers to search for more advanced techniques such as mass spectrometry (MS). MS has provided a methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level.

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Article Chemistry, Analytical

SALDI-MS and SERS Multimodal Imaging: One Nanostructured Substrate to Rule Them Both

Stefania-Alexandra Iakab et al.

Summary: This study presents a multimodal imaging approach that combines surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) and surface-enhanced Raman spectroscopy (SERS) using a gold-coated nanostructured silicon substrate. By using the same substrate, sample preparation, and data analysis software, both imaging modalities can be integrated and co-registered on the same sample. The approach was successfully applied to analyze the chemical composition and distribution of molecules transferred from clean fingertips and fingertips covered with plasticine modeling clay, providing valuable information on the composition of the clay and locating the traces of plasticine on fingermarks.

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Review Chemistry, Applied

Isolation and functionalities of bioactive peptides from fruits and vegetables: A reviews

Chandana Sosalagere et al.

Summary: Bioactive peptides are receiving increasing research attention as potential therapies for managing bodily disorders and metabolic syndromes, while there is a global trend towards the consumption of fruits and vegetables for dietary and health needs. This review emphasizes on the isolation and bio-functional properties of bioactive peptides from fruits and vegetables.

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Review Biotechnology & Applied Microbiology

Anti-obesity drug discovery: advances and challenges

Timo D. Mueller et al.

Summary: Enormous progress has been made in managing diseases associated with excess body weight, but treatment of obesity itself remains challenging. By summarizing the history and advancements in anti-obesity medications, researchers are now pursuing next-generation AOMs that could safely and effectively achieve weight loss.

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Article Biochemistry & Molecular Biology

Database resources of the national center for biotechnology information

Eric W. Sayers et al.

Summary: The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including databases for nucleic acid sequences and life science journal citations. It provides search and retrieval operations for most of these data from 35 distinct databases, with E-utilities serving as the programming interface. Several resources received significant updates in the past year.

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Article Biochemistry & Molecular Biology

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

Beatrice Amos et al.

Summary: VEuPathDB project is a bioinformatics resource center funded by the National Institutes of Health, supporting over 500 organisms including invertebrate vectors, eukaryotic pathogens, and hosts. It integrates over 1700 pre-analyzed datasets, providing advanced search capabilities, visualizations, and analysis tools, with standardized workflows for researchers to access Omics data and bioinformatic analyses.

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Article Chemistry, Multidisciplinary

Natural product drug discovery in the artificial intelligence era

F. I. Saldivar-Gonzalez et al.

Summary: Natural products are considered privileged structures to interact with protein drug targets, sparking interest in developing NP-inspired medicines. The advancement of artificial intelligence has democratized the field of natural product drug discovery, with the introduction of natural language processing and machine learning algorithms enhancing molecular design and target selectivity.

CHEMICAL SCIENCE (2022)

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Article Microbiology

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Robert H. Mills et al.

Summary: Multi-omics analysis of faecal samples from patients with ulcerative colitis suggests a connection between Bacteroides vulgatus protease activity and the severity of disease symptoms. Understanding the disruption of host-microbiota interactions in UC is crucial for developing effective treatments. The study demonstrates that the overabundance of B. vulgatus proteases in a subset of UC patients contributes to disease activity. Targeting the protease activity could be a potential strategy for treating UC.

NATURE MICROBIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Dysregulation of Neuropeptide and Tau Peptide Signatures in Human Alzheimer?s Disease Brain

Sonia Podvin et al.

Summary: This study evaluated neuropeptide signatures and tau peptide signatures in Alzheimer's disease (AD) brains compared to age-matched controls. The results showed distinct profiles of neuropeptides and unique tau peptides in AD, indicating differences in proteolytic processing. These findings suggest that the dysregulation of neuropeptides and tau peptides may contribute to the cognitive deficits observed in AD.

ACS CHEMICAL NEUROSCIENCE (2022)

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Article Chemistry, Applied

Major shrimp allergen peptidomics signatures and potential biomarkers of heat processing

Li Li Xu et al.

Summary: This study provides new insights into the structural effects of processing on major shrimp allergens and peptide candidates as processing biomarkers, by analyzing the impact of different processing methods on shrimp allergenic peptides.

FOOD CHEMISTRY (2022)

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Article Biochemistry & Molecular Biology

Profiling 26,000 Aplysia californica neurons by single cell mass spectrometry reveals neuronal populations with distinct neuropeptide profiles

Peter C. Chan-Andersen et al.

Summary: This study used microscopy-guided, high-throughput mass spectrometry to investigate the neuropeptide heterogeneity in the California sea hare. They identified 40 unique neuronal populations with distinct neuropeptide profiles, some of which were behaviorally related. This mass spectrometry-based approach offers a robust categorization of large cell populations based on single cell neuropeptide content and can be applied to various animals and tissues.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

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Review Pharmacology & Pharmacy

Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics

Krishna D. B. Anapindi et al.

Summary: The discovery of insulin in the early 1900s led to the exploration of the role of peptides as hormones and neuromodulators. These gene products can be found in all organisms and play important roles in coordinating complex physiology and behavior. Misregulation of peptides has been linked to various diseases. Through the use of animal models and modern technologies, we can gain mechanistic insight into endogenous peptides and translate that knowledge into medical applications. Advances in medicine and basic science have influenced the definition of signaling peptides and paved the way for drug development. Peptide biologics have become valuable drugs due to their specificity, lack of toxic metabolites, and minimal side effects.

PHARMACOLOGICAL REVIEWS (2022)

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Review Biochemical Research Methods

Recent advances in isobaric labeling and applications in quantitative proteomics

Michael K. Sivanich et al.

Summary: This article provides an overview of the application of mass spectrometry (MS) in quantitative proteomics. Liquid chromatography-mass spectrometry (LC-MS) is a powerful technique for accurately quantifying proteins and peptides in complex biological samples. Isobaric tagging, a commonly used chemical isotopic labeling technique, allows for quantification based on MS2 peptide analysis. The article also discusses recent developments in isobaric tagging methods and improvements, as well as limitations and approaches to address them. The review highlights the diverse applications of isobaric tags in biomarker discovery, thermal proteome profiling, cross-linking structural investigations, single-cell analysis, top-down proteomics, and analysis of neuropeptides, glycans, metabolites, and lipids. Considerations and evaluations are provided for each application.

PROTEOMICS (2022)

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Native metabolomics identifies the rivulariapeptolide family of protease inhibitors

Raphael Reher et al.

Summary: The identity and biological activity of most metabolites are still unknown, and compound purification is a bottleneck for exploring their structures and pharmaceutical activities. Using a scalable native metabolomics approach, we identified a class of potentially bioactive metabolites and conducted structural elucidation and biological activity evaluation.

NATURE COMMUNICATIONS (2022)

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Article Infectious Diseases

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage

Diana Lin et al.

Summary: Antibiotic resistance is a global health crisis, and alternative antimicrobial therapeutics are urgently needed. This study presents rAMPage, a bioinformatics discovery platform, to identify AMP sequences from RNA-seq datasets. The researchers used rAMPage on 84 publicly available RNA-seq datasets, identifying 1137 possible AMPs, with 1024 deemed novel. Testing 21 selected peptide sequences, seven of them showed high antimicrobial activity.

ANTIBIOTICS-BASEL (2022)

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Review Biotechnology & Applied Microbiology

Designer bacterial cell factories for improved production of commercially valuable non-ribosomal peptides

Sayak Mitra et al.

Summary: Non-ribosomal peptides (NRPs) are secondary metabolites with high commercial importance. However, the low synthesis yield by bacteria and losses during purification hinder their industrial-scale production. This review discusses strategies for enhancing NRP yield, including isolation of efficient producer strains, optimization of bioprocesses, and the use of metabolic engineering and synthetic biology techniques to redirect metabolic network fluxes. The review also provides insights into the regulation of NRP biosynthesis and highlights the potential of computational techniques in designing cellular factories for NRP production.

BIOTECHNOLOGY ADVANCES (2022)

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Article Biochemistry & Molecular Biology

BioCAT: Search for biosynthetic gene clusters producing nonribosomal peptides with known structure

Dmitry N. Konanov et al.

Summary: This study developed a tool called BioCAT for finding biosynthetic gene clusters that may produce nonribosomal peptides. By implementing a position-specific score matrix, the method increased alignment sensitivity and was validated on a curated database and other examples.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2022)

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Article Biochemical Research Methods

DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction

Yu Zhang et al.

Summary: The development of deep sequencing technologies has led to the discovery of novel transcripts. Many methods have been developed for assessing the coding potential of these transcripts, with DeepCPP being a deep learning method that outperforms other state-of-the-art methods, especially on sORF type data. The use of discontinuous k-mer, nucleotide bias, and minimal distribution similarity feature selection methods proved crucial in improving the accuracy of coding potential prediction for RNA.

BRIEFINGS IN BIOINFORMATICS (2021)

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Review Endocrinology & Metabolism

Neuromodulatory pathways in learning and memory: Lessons from invertebrates

Sara Van Damme et al.

Summary: Animals must continuously adapt to changes in their environment, with learning and memory playing a crucial role in enhancing survival chances. Neuromodulators, particularly monoamines and neuropeptides, influence learning and memory, though our understanding of their functions remains limited. The conservation of neuromodulatory systems and their effects on learning circuits in invertebrates provide valuable insights for understanding pathways involved in learning and memory.

JOURNAL OF NEUROENDOCRINOLOGY (2021)

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Article Biochemistry & Molecular Biology

Importance of the Cyclic Cystine Knot Structural Motif for Immunosuppressive Effects of Cyclotides

Roland Hellinger et al.

Summary: This study provides novel functional data and mechanistic insights into structure-activity relationships of the cyclotide T20K, showing that the cyclic cystine knot motif in cyclotides governs their bioactivity, interactions with cell membranes, and transport across biological membranes. These findings could be useful for understanding the structure-activity of other cystine knot proteins and guiding the design of novel cysteine-stabilized molecules.

ACS CHEMICAL BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Bioinformatics-Guided Expansion and Discovery of Graspetides

Sangeetha Ramesh et al.

Summary: Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products that are formed through ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications are derived from different amino acid residues and characterized graspetides include serine protease inhibitors.

ACS CHEMICAL BIOLOGY (2021)

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Review Biochemistry & Molecular Biology

Advancing D-amino acid-containing peptide discovery in the metazoan

David H. Mast et al.

Summary: The discovery of enzyme-derived D-amino acid-containing peptides challenges assumptions about the homochirality of animal proteins and presents new analytical challenges in peptide structural and functional characterization. Most known DAACPs have been identified through laborious purification studies or homology to previously identified ones. High throughput mass spectrometry-based peptidomics dominate peptide characterization experiments, with stereochemistry rarely considered due to technical challenges of identifying L/D isomerization, suggesting that more DAACPs remain to be uncovered.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2021)

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Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemistry & Molecular Biology

Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in Cancer borealis

Kellen DeLaney et al.

Summary: The study utilized a multifaceted mass spectrometry approach to identify neuropeptides that differentiate feeding states in the Cancer borealis nervous system. The research revealed differences in spatial distribution and abundance of specific neuropeptides in the brain and neuroendocrine pericardial organs between fed and unfed animals. These findings provide valuable opportunities for future functional studies on neuropeptides influencing feeding-related behaviors.

ACS CHEMICAL NEUROSCIENCE (2021)

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Article Biochemical Research Methods

Removal of optimal cutting temperature (OCT) compound from embedded tissue for MALDI imaging of lipids

Jacob X. M. Truong et al.

Summary: MALDI-MSI is a molecular imaging technique used to study the abundance and distribution of lipids in tissues. Challenges in sample pre-treatment and preparation have hindered the analysis of clinical tissues. A new method has been developed to remove O.C.T. and endogenous salts simultaneously, preventing analyte suppression, simplifying data interpretation, and improving sensitivity.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2021)

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Article Biochemistry & Molecular Biology

Transcriptomic, peptidomic, and mass spectrometry imaging analysis of the brain in the ant Cataglyphis nadus

Jens Habenstein et al.

Summary: This study identified neuropeptides in the Cataglyphis nodus ants and characterized their spatial distribution in the ant brain using advanced imaging techniques. The research provides a foundation for future studies on behavioral transitions and the functional role of neuropeptides in Cataglyphis ants.

JOURNAL OF NEUROCHEMISTRY (2021)

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Article Biochemical Research Methods

Targeted Top-Down Mass Spectrometry for the Characterization and Tissue-Specific Functional Discovery of Crustacean Hyperglycemic Hormones (CHH) and CHH Precursor-Related Peptides in Response to Low pH Stress

Yang Liu et al.

Summary: This study characterized two CHH isoforms from the Atlantic blue crab using a targeted top-down approach, and monitored the response of CHHs and CPRP under low pH stress using label-free and isotopic labeling methods. CPRP could serve as an ideal probe for tracking changes in CHH expression levels, simplifying quantitative analysis. The tissue-specific functions of CHHs in the regulation of low pH stress were demonstrated by distinct expression patterns in the sinus glands and pericardial organs. Ion mobility-mass spectrometry was employed for conformation analysis of CHHs and CPRPs from different tissues.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2021)

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Article Biotechnology & Applied Microbiology

Trends in peptide drug discovery

Markus Muttenthaler et al.

Summary: This Perspective summarizes key trends in peptide drug discovery and development, including human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry. It also emphasizes lessons from earlier approaches that are still relevant today and discusses emerging strategies impact on peptide drug discovery.

NATURE REVIEWS DRUG DISCOVERY (2021)

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Review Engineering, Biomedical

Broad-Spectrum Antiviral Peptides and Polymers

Agnes Kuroki et al.

Summary: The necessity of developing broad-spectrum antiviral agents against emerging and re-emerging viruses is discussed, along with the recent advancements in antiviral peptides and polymers. Future perspectives include the development of virucidal peptides/polymers for combating SARS-CoV-2 infection, standardization of antiviral testing protocols, and the use of artificial intelligence or machine learning to accelerate the discovery of antiviral macromolecules.

ADVANCED HEALTHCARE MATERIALS (2021)

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Article Chemistry, Analytical

Analysis of Peptide Stereochemistry in Single Cells by Capillary Electrophoresis-Trapped Ion Mobility Spectrometry Mass Spectrometry

David H. Mast et al.

Summary: Single cell analysis investigates molecular heterogeneity in morphologically similar cell populations through quantitative or qualitative measurements of genetic, proteomic, or metabolic products. This study utilized capillary electrophoresis with mass spectrometry to characterize peptide content in single cells, revealing important physiological consequences of peptide isomerization. The findings demonstrate an unusual distribution of isomerized peptides in A. californica and establish CE-TIMS MS as a powerful analytical tool for investigating peptide stereochemistry at the single cell level.

ANALYTICAL CHEMISTRY (2021)

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Review Biochemistry & Molecular Biology

Recent developments in sustainably sourced protein-based biomaterials

H. Agnieray et al.

Summary: Research on sustainable biomaterials is growing in importance due to the increased demand for materials with reduced environmental impact. This field utilizes natural, renewable resources to develop innovative materials that encompass the entire material life cycle. Proteins such as collagen, gelatin, keratin, and silk show promise as biocompatible and biodegradable materials for various applications.

BIOCHEMICAL SOCIETY TRANSACTIONS (2021)

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Article Biology

A conserved neuropeptide system links head and body motor circuits to enable adaptive behavior

Shankar Ramachandran et al.

Summary: This study reveals how the Caenorhabditis elegans NLP-12 neuropeptide system shapes responses to food availability by modulating the activity of head and body wall motor neurons through G-protein coupled receptor targets CKR-1 and CKR-2. The research shows that CKR-1 and CKR-2 play important roles in regulating locomotor responses to changing food availability.

ELIFE (2021)

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Article Genetics & Heredity

Identification of Non-Canonical Translation Products in C. elegans Using Tandem Mass Spectrometry

Bhavesh S. Parmar et al.

Summary: Transcriptome and ribosome sequencing have identified numerous non-canonical transcripts in C. elegans, leading to the discovery of a large number of non-canonical proteins and splice variants through tandem mass spectrometry. Diverse proteomic and peptidomic strategies have also helped in detecting additional novel non-canonical proteins, providing a valuable resource for further research.

FRONTIERS IN GENETICS (2021)

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Article Biochemistry & Molecular Biology

Nerpa: A Tool for Discovering Biosynthetic Gene Clusters of Bacterial Nonribosomal Peptides

Olga Kunyavskaya et al.

Summary: Microbial natural products, especially nonribosomal peptides, are a diverse class of bioactive compounds for drug discovery. The computational method Nerpa has been developed to discover and link novel biosynthetic gene clusters responsible for producing known nonribosomal peptides, enhancing our understanding of their synthesis and biosynthetic enzymes.

METABOLITES (2021)

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Article Biochemical Research Methods

In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease

Zhengwei Chen et al.

Summary: A novel N-glycoproteomic approach was developed in this study and successfully applied to analyze human cerebrospinal fluid samples, identifying a large number of intact N-glycopeptides and providing a molecular basis for understanding the structure-function relationships and disease mechanisms related to glycoproteins in cerebrospinal fluid. Additionally, a comparative in-depth N-glycoproteomic analysis of cerebrospinal fluid samples from healthy controls and Alzheimer's disease patients revealed altered glycosylation patterns for several N-glycoproteins, suggesting potential targets for further studies on glycosylation-based Alzheimer's disease research.

MOLECULAR & CELLULAR PROTEOMICS (2021)

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Article Biochemistry & Molecular Biology

EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure

Marius Alfred Dieckmann et al.

Summary: The EDGAR platform is a web server offering precomputed orthology data for thousands of microbial genomes, playing a crucial role in comparative genomics and phylogenomics research. With advanced technical infrastructure and features like Venn diagrams and phylogenetic trees, EDGAR 3.0 introduces scalable infrastructure for comprehensive microbial comparative gene content analysis, accommodating the increasing number of genomes analyzed in projects.

NUCLEIC ACIDS RESEARCH (2021)

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Review Neurosciences

Neuropeptide Localization in Lymnaea stagnalis: From the Central Nervous System to Subcellular Compartments

Ellen A. Wood et al.

Summary: The great pond snail Lymnaea stagnalis is a well-established model organism with a simple central nervous system that has been extensively used to study neural functioning. Through electrophysiological experiments and mass spectrometry techniques, researchers have mapped neuronal connections and identified circuits responsible for basic life functions. This combination of techniques has led to increasing insights into the molecular basis of CNS-controlled biological functions.

FRONTIERS IN MOLECULAR NEUROSCIENCE (2021)

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Review Chemistry, Multidisciplinary

Microfluidics for Peptidomics, Proteomics, and Cell Analysis

Rui Vitorino et al.

Summary: Microfluidics is an advanced microtechnology for manipulating fluids in small channels, offering tools for controlling chemical, biological, and physical processes. It plays a crucial role in various fields and is often combined with mass spectrometry for analysis. Recent developments include applications in proteomics, peptidomics, cell analysis, and detection methods for clinical questions.

NANOMATERIALS (2021)

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Article Biochemistry & Molecular Biology

Differential Neuropeptidomes of Dense Core Secretory Vesicles (DCSV) Produced at Intravesicular and Extracellular pH Conditions by Proteolytic Processing

Zhenze Jiang et al.

Summary: This study investigated the production of neuropeptides within cells at different pH conditions and found that distinct neuropeptidomes are generated at internal and external pH levels. Various types of proteases play a role in regulating neuropeptide formation.

ACS CHEMICAL NEUROSCIENCE (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

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Article Biotechnology & Applied Microbiology

MaxDIA enables library-based and library-free data-independent acquisition proteomics

Pavel Sinitcyn et al.

Summary: MaxDIA is a software platform specifically designed for analyzing DIA proteomics data within the MaxQuant environment, achieving deep proteome coverage and improved protein quantification accuracy. It provides accurate FDR estimates for hypothesis-free analysis of DIA samples.

NATURE BIOTECHNOLOGY (2021)

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Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

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Article Toxicology

Venom peptides - A comprehensive translational perspective in pain management

V. Vidya et al.

Summary: Venom peptides have shown potential therapeutic effects by modulating various targets, with research progress made in clinical development targeting different diseases. Understanding venomous animals, their venoms, and pharmacological effects contributes to a better grasp of their therapeutic prospects.

CURRENT RESEARCH IN TOXICOLOGY (2021)

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Article Chemistry, Multidisciplinary

Improvement of the antimicrobial potency, pharmacokinetic and pharmacodynamic properties of albicidin by incorporation of nitrogen atoms

Lieby Zborovsky et al.

Summary: The study reported the design and synthesis of new albicidins with N-atoms, showing enhanced antibacterial activity and spectrum, particularly against Gram-positive bacteria. Density functional theory calculations were used to find the most stable conformation of each derivative. In vivo experiments with an albicidin analogue demonstrated promising pharmacokinetics, lack of toxicity, and efficacy in reducing bacterial titers in an E. coli infection model with fluoroquinolone-resistant strains, highlighting the potential of albicidins as active antibacterial agents.

CHEMICAL SCIENCE (2021)

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Article Biochemical Research Methods

Genomics- and Peptidomics-Based Discovery of Conserved and Novel Neuropeptides in the American Cockroach

Huanchao Zeng et al.

Summary: Through an integrated approach of genomics and peptidomics, this study identified 35 conserved neuropeptides and a potential novel neuropeptide in the American cockroach. The research provides a comprehensive neuropeptidome and detailed spatiotemporal distribution patterns, laying a solid foundation for future functional studies of neuropeptides in this insect species.

JOURNAL OF PROTEOME RESEARCH (2021)

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Article Biochemistry & Molecular Biology

DDBJ update: streamlining submission and access of human data

Asami Fukuda et al.

Summary: The DDBJ Center provides diverse biological databases and the NIG supercomputer for life sciences research. Collaborating with NCBI, EBI, and NBDC, it manages nucleotide sequences and human genotype-phenotype data.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biochemical Research Methods

De novo prediction of the elemental composition of peptides and proteins based on a single mass

Jurgen Claesen et al.

JOURNAL OF MASS SPECTROMETRY (2020)

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Article Biochemical Research Methods

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

Vadim Demichev et al.

NATURE METHODS (2020)

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Article Biochemistry & Molecular Biology

Differential Post-Translational Amino Acid Isomerization Found among Neuropeptides in Aplysia californica

David H. Mast et al.

ACS CHEMICAL BIOLOGY (2020)

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Review Pharmacology & Pharmacy

Novel approaches leading towards peptide GPCR de-orphanisation

Alexander S. Hauser et al.

BRITISH JOURNAL OF PHARMACOLOGY (2020)

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Article Plant Sciences

Discovery and Characterization of a PKS-NRPS Hybrid in Aspergillus terreus by Genome Mining

Shen Tang et al.

JOURNAL OF NATURAL PRODUCTS (2020)

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Article Biochemical Research Methods

Temporal Study of the Perturbation of Crustacean Neuropeptides Due to Severe Hypoxia Using 4-Plex Reductive Dimethylation

Amanda R. Buchberger et al.

JOURNAL OF PROTEOME RESEARCH (2020)

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Article Multidisciplinary Sciences

DeepRiPP integrates multiomics data to automate discovery of novel ribosomally synthesized natural products

Nishanth J. Merwin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Chemistry, Analytical

CycloBranch 2: Molecular Formula Annotations Applied to imzML Data Sets in Bimodal Fusion and LC-MS Data Files

Jiri Novak et al.

ANALYTICAL CHEMISTRY (2020)

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Review Biochemistry & Molecular Biology

Breaking a Couple: Disulfide Reducing Agents

Sinenhlanhla N. Mthembu et al.

CHEMBIOCHEM (2020)

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Article Biochemical Research Methods

Optimal Dissociation Methods Differ for N- and O-Glycopeptides

Nicholas M. Riley et al.

JOURNAL OF PROTEOME RESEARCH (2020)

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Article Biochemistry & Molecular Biology

A Quantitative Proteome Map of the Human Body

Lihua Jiang et al.

CELL (2020)

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Review Chemistry, Multidisciplinary

Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms

Anthony J. Metrano et al.

CHEMICAL REVIEWS (2020)

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Article Microbiology

Estimate of the sequenced proportion of the global prokaryotic genome

Zheng Zhang et al.

MICROBIOME (2020)

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Article Chemistry, Analytical

Automatic Annotation and Dereplication of Tandem Mass Spectra of Peptidic Natural Products

Emma Ricart et al.

ANALYTICAL CHEMISTRY (2020)

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Article Biotechnology & Applied Microbiology

Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering

Mohamed Helmy et al.

METABOLIC ENGINEERING COMMUNICATIONS (2020)

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Article Chemistry, Analytical

Capillary electrophoresis coupled to MALDI mass spectrometry imaging with large volume sample stacking injection for improved coverage of C. borealis neuropeptidome

Kellen DeLaneya et al.

ANALYST (2020)

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Article Chemistry, Analytical

Site-Specific Glycosylation Quantitation of 50 Serum Glycoproteins Enhanced by Predictive Glycopeptidomics for Improved Disease Biomarker Discovery

Qiongyu Li et al.

ANALYTICAL CHEMISTRY (2019)

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Article Biochemical Research Methods

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Laurent Heirendt et al.

NATURE PROTOCOLS (2019)

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Glycosylation in health and disease

Colin Reily et al.

NATURE REVIEWS NEPHROLOGY (2019)

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rBAN: retro-biosynthetic analysis of nonribosomal peptides

Emma Ricart et al.

JOURNAL OF CHEMINFORMATICS (2019)

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antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2019)

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Article Biochemical Research Methods

pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework

Hao Yang et al.

BIOINFORMATICS (2019)

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Review Biochemistry & Molecular Biology

Antiviral peptides as promising therapeutic drugs

Liana Costa Pereira Vilas Boas et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2019)

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Article Multidisciplinary Sciences

Seasonal adaptations of the hypothalamo-neurohypophyseal system of the dromedary camel

Fatma Zohra Djazouli Alim et al.

PLOS ONE (2019)

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Article Genetics & Heredity

EvoMining reveals the origin and fate of natural product biosynthetic enzymes

Nelly Selem-Mojica et al.

MICROBIAL GENOMICS (2019)

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Article Biochemistry & Molecular Biology

A deep learning genome-mining strategy for biosynthetic gene cluster prediction

Geoffrey D. Hannigan et al.

NUCLEIC ACIDS RESEARCH (2019)

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Article Biochemical Research Methods

MiPepid: MicroPeptide identification tool using machine learning

Mengmeng Zhu et al.

BMC BIOINFORMATICS (2019)

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Article Biochemistry & Molecular Biology

Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors

Simon R. Foster et al.

CELL (2019)

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Review Chemistry, Multidisciplinary

Conotoxins: Chemistry and Biology

Ai-Hua Jin et al.

CHEMICAL REVIEWS (2019)

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Article Biochemical Research Methods

PACAP and Other Neuropeptide Targets Link Chronic Migraine and Opioid-induced Hyperalgesia in Mouse Models

Krishna D. B. Anapindi et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

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Article Multidisciplinary Sciences

A new antibiotic selectively kills Gram-negative pathogens

Yu Imai et al.

NATURE (2019)

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Article Multidisciplinary Sciences

Structural characterization of scorpion peptides and their bactericidal activity against clinical isolates of multidrug-resistant bacteria

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Molecular insights into the interaction of hemorphin and its targets

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Peptidome analysis reveals the involvement of endogenous peptides in mouse pancreatic dysfunction with aging

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Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry

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Protein Data Bank: the single global archive for 3D macromolecular structure data

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Gentle Introduction to the Statistical Foundations of False Discovery Rate in Quantitative Proteomics

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Shedding Light on the Molecular Pathology of Amyloid Plaques in Transgenic Alzheimer's Disease Mice Using Multimodal MALDI Imaging Mass Spectrometry

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Diversity of Neuropeptide Cell-Cell Signaling Molecules Generated by Proteolytic Processing Revealed by Neuropeptidomics Mass Spectrometry

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Neuropeptide Mapping of Dimmed Cells of Adult Drosophila Brain

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cAMP, Ca2+, pH(i), and NO Regulate H-like Cation Channels That Underlie Feeding and Locomotion in the Predatory Sea Slug Pleurobranchaea californica

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Reagents for Isobaric Labeling Peptides in Quantitative Proteomics

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Aplysia allatotropin-related peptide and its newly identified d-amino acid-containing epimer both activate a receptor and a neuronal target

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Dereplication of peptidic natural products through database search of mass spectra

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FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

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Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes

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Targeted Mass Spectrometry Approach Enabled Discovery of O-Glycosylated Insulin and Related Signaling Peptides in Mouse and Human Pancreatic Islets

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Bioactive Peptide Natural Products as Lead Structures for Medicinal Use

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Nonribosomal Peptide Synthesis-Principles and Prospects

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Culture-independent discovery of natural products from soil metagenomes

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Aspects of Quantitation in Mass Spectrometry Imaging Investigated on Cryo-Sections of Spiked Tissue Homogenates

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Systematic Errors in Peptide and Protein Identification and Quantification by Modified Peptides

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Peptidomics of Circular Cysteine-Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining

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Novel isotopic N,N-Dimethyl Leucine (iDiLeu) Reagents Enable Absolute Quantification of Peptides and Proteins Using a Standard Curve Approach

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OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

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Cyclotide Discovery in Gentianales Revisited-Identification and Characterization of Cyclic Cystine-Knot Peptides and Their Phylogenetic Distribution in Rubiaceae Plants

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Neuropeptides and Epitheliopeptides: Structural and Functional Diversity in an Ancestral Metazoan Hydra

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Quantitative Glycoproteomic Analysis of Optimal Cutting Temperature-Embedded Frozen Tissues Identifying Glycoproteins Associated with Aggressive Prostate Cancer

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Desorption Electrospray Ionization then MALDI Mass Spectrometry Imaging of Lipid and Protein Distributions in Single Tissue Sections

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Deuterium Isobaric Amine-Reactive Tags for Quantitative Proteomics

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Ligand-Based Peptide Design and Combinatorial Peptide Libraries to Target G Protein-Coupled Receptors

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CURRENT PHARMACEUTICAL DESIGN (2010)

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Naturally Occurring Human Urinary Peptides for Use in Diagnosis of Chronic Kidney Disease

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Heat Stabilization of the Tissue Proteome: A New Technology for Improved Proteomics

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Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

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Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues

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Selected reaction monitoring for quantitative proteomics: a tutorial

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Article Physics, Atomic, Molecular & Chemical

Artifacts of MALDI sample preparation investigated by high-resolution scanning microprobe matrix-assisted laser desorption/ionization (SMALDI) imaging mass spectrometry

Werner Bouschen et al.

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY (2007)

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Article Engineering, Biomedical

Multivariate analysis strategies for processing ToF-SIMS images of biomaterials

Bonnie J. Tyler et al.

BIOMATERIALS (2007)

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Review Biochemical Research Methods

Chromatographic techniques for the separation of peptides: Application to proteomics

Srinubabu Gedela et al.

CHROMATOGRAPHIA (2007)

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Article Biochemical Research Methods

Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research

Sebastian Wiese et al.

PROTEOMICS (2007)

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Article Biochemical Research Methods

Optimization of mass spectrometry-compatible surfactants for shotgun proteomics

Emily I. Chen et al.

JOURNAL OF PROTEOME RESEARCH (2007)

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Article Biochemical Research Methods

Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections

R. Lemaire et al.

JOURNAL OF PROTEOME RESEARCH (2007)

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Article Chemistry, Analytical

MALDI-MS direct tissue analysis of proteins: improving signal sensitivity using organic treatments

R. Lemaire et al.

ANALYTICAL CHEMISTRY (2006)

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Article Biochemical Research Methods

Peptidomics analysis of neuropeptides involved in copulatory behavior of the mollusk Lymnaea stagnalis

Z. El Filali et al.

JOURNAL OF PROTEOME RESEARCH (2006)

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Review Biochemical Research Methods

Machine learning in bioinformatics

Pedro Larranaga et al.

BRIEFINGS IN BIOINFORMATICS (2006)

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Article Neurosciences

Peptidomics of a single identified neuron reveals diversity of multiple neuropeptides with convergent actions on cellular excitability

CR Jiménez et al.

JOURNAL OF NEUROSCIENCE (2006)

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Review Biochemical Research Methods

Fluorescence microscopy

JW Lichtman et al.

NATURE METHODS (2005)

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Article Biochemical Research Methods

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein

Y Ishihama et al.

MOLECULAR & CELLULAR PROTEOMICS (2005)

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Article Biochemistry & Molecular Biology

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

J Besemer et al.

NUCLEIC ACIDS RESEARCH (2005)

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Review Pathology

Technical aspects of immunohistochemistry

JA Ramos-Vara

VETERINARY PATHOLOGY (2005)

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Article Biochemistry & Molecular Biology

The EMBL nucleotide sequence database

C Kanz et al.

NUCLEIC ACIDS RESEARCH (2005)

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Review Biochemical Research Methods

Peptidomics

G Baggerman et al.

JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2004)

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Review Biochemical Research Methods

Peptide separation by Hydrophilic-Interaction Chromatography: a review

T Yoshida

JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS (2004)

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Article Chemistry, Analytical

Stable-isotope dimethyl labeling for quantitative proteomics

JL Hsu et al.

ANALYTICAL CHEMISTRY (2003)

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Article Biochemical Research Methods

Direct tissue analysis using matrix-assisted laser desorption/ionization mass spectrometry: practical aspects of sample preparation

SA Schwartz et al.

JOURNAL OF MASS SPECTROMETRY (2003)

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Article Multidisciplinary Sciences

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

SA Gerber et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

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Article Chemistry, Analytical

Tandem mass tags:: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS

A Thompson et al.

ANALYTICAL CHEMISTRY (2003)

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Review Chemistry, Multidisciplinary

The desorption process in MALDI

K Dreisewerd

CHEMICAL REVIEWS (2003)

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Article Biotechnology & Applied Microbiology

Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry

DK Han et al.

NATURE BIOTECHNOLOGY (2001)

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Article Chemistry, Analytical

Proteolytic 18O labeling for comparative proteomics:: Model studies with two serotypes of adenovirus

XD Yao et al.

ANALYTICAL CHEMISTRY (2001)

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