☆ 4.3 Article

Empowering peptidomics: utilizing computational tools and approaches

BIOANALYSIS (2023)

Related references

Note: Only part of the references are listed.

Article Biochemical Research Methods

A peptide-centric approach to analyse quantitative proteomics data- an application to prostate cancer biomarker discovery

Tania Lima et al.

Summary: This study reanalyzed a urine proteome dataset from prostate cancer patients and controls using a peptide-centric approach. Compared to the conventional protein-centric approach, the peptide analysis revealed more relevant information related to prostate cancer, highlighting the importance of peptide analysis in proteomics research.

JOURNAL OF PROTEOMICS (2023)

Add to Collection

Review Genetics & Heredity

Insights from multi-omics integration in complex disease primary tissues

Peter Kreitmaier et al.

Summary: Genome-wide association studies have revealed the genetic basis of complex diseases, and multi-omics approaches can characterize molecular profiles in relevant tissues to understand disease mechanisms. This article highlights progress in integrating studies on type 2 diabetes, osteoarthritis, Alzheimer's disease, and systemic lupus erythematosus. High-resolution techniques like single-cell and spatial omics will be crucial in the future, and it is important to include understudied cell types and diverse populations.

TRENDS IN GENETICS (2023)

Add to Collection

Review Biochemistry & Molecular Biology

Advances in Ultra-High-Resolution Mass Spectrometry for Pharmaceutical Analysis

Estelle Deschamps et al.

Summary: Pharmaceutical analysis is a complex science that involves various disciplines and covers drug development to its impact on health and the environment. The pharmaceutical industry is heavily regulated, requiring powerful analytical instrumentation and efficient methods. Mass spectrometry, especially ultra-high-resolution mass spectrometry with Fourier transform instruments, has been increasingly used in pharmaceutical analysis for research and routine quality controls. This review summarizes the principles and applications of Fourier transform mass spectrometers in pharmaceutical analysis.

MOLECULES (2023)

Add to Collection

Article Chemistry, Multidisciplinary

Discovery Proteomics and Absolute Protein Quantification Can Be Performed Simultaneously on an Orbitrap-Based Mass Spectrometer

Taufika Islam Williams et al.

Summary: Mass spectrometry plays an important role in quantification-centered protein research, and protein cleavage isotope dilution MS is a reliable method for quantifying proteins. In our study, we compared data-dependent acquisition (DDA) and parallel reaction monitoring (PRM) workflows for quantifying egg yolk protein precursors or vitellogenins (VTGs) in striped bass. Our results show that there is no statistical difference between MS1-based and MS2-based VTG quantification.

ACS OMEGA (2023)

Add to Collection

Article Oncology

Application of Proteogenomics to Urine Analysis towards the Identification of Novel Biomarkers of Prostate Cancer: An Exploratory Study

Tania Lima et al.

Summary: This study utilized proteomics and proteogenomics approaches to identify dysregulated mutant protein isoforms in urine from prostate cancer patients. These findings offer promising opportunities for the research and development of non-invasive biomarkers for prostate cancer detection.

CANCERS (2022)

Add to Collection

Review Biochemistry & Molecular Biology

Peptidomic Approaches and Observations in Neurodegenerative Diseases

Besnik Muqaku et al.

Summary: Mass spectrometry is an important technique for analyzing biomolecules, especially in the field of neurodegenerative diseases where peptidomics analysis of cerebrospinal fluid samples has played a crucial role.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Add to Collection

Article Multidisciplinary Sciences

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

Mathias Walzer et al.

Summary: This study introduces a re-analysis pipeline for public SWATH-MS datasets, which includes automated workflows and statistical analysis, and integrates the results into the Expression Atlas resource. By reanalysing 10 public DIA datasets, the robustness of the pipeline was validated, and the final results were integrated into Expression Atlas.

SCIENTIFIC DATA (2022)

Add to Collection

Review Biochemistry & Molecular Biology

Discovering the landscape of protein modifications

Keith E. Keenan et al.

Summary: Protein modifications play a significant role in cell biology across various organisms. Discoveries in the early 20th century challenged traditional definitions of amino acids, and the advent of mass-spectrometry-based proteomics in the latter part led to a rapid increase in known protein modifications, with over 500 identified today. New computational tools in data science, machine learning, and artificial intelligence are expected to further advance the discovery and understanding of protein modifications in the future.

MOLECULAR CELL (2021)

Add to Collection

Review Biochemistry & Molecular Biology

Role of Peptides in Diagnostics

Shashank Pandey et al.

Summary: This article discusses the application of synthetic peptides in diagnostics, including imaging and non-imaging diagnostics; introduces the peptide-based ELISA technology and the use of peptides in imaging techniques; emphasizes the advantages and disadvantages of peptides; also explores the application of peptides in deadly diseases such as COVID-19 and cancer.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Add to Collection

Article Biochemical Research Methods

Assessing Protein Sequence Database Suitability Using De Novo Sequencing

Richard S. Johnson et al.

MOLECULAR & CELLULAR PROTEOMICS (2020)

Add to Collection

Review Chemistry, Medicinal

Machine intelligence in peptide therapeutics: A next-generation tool for rapid disease screening

Shaherin Basith et al.

MEDICINAL RESEARCH REVIEWS (2020)

Add to Collection

Review Spectroscopy

A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation

Thomas De Vijlder et al.

MASS SPECTROMETRY REVIEWS (2018)

Add to Collection

Review Biochemical Research Methods

Digging Deep into Peptidomics Applied to Body Fluids

Rui Vitorino

PROTEOMICS (2018)

Add to Collection

Article Chemistry, Analytical

Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data

Zhibin Ning et al.

ANALYTICAL CHEMISTRY (2016)

Add to Collection

Article Chemistry, Analytical

Evolution of Orbitrap Mass Spectrometry Instrumentation

Shannon Eliuk et al.

ANNUAL REVIEW OF ANALYTICAL CHEMISTRY, VOL 8 (2015)

Add to Collection

Article Biochemical Research Methods

Novor: Real-Time Peptide de Novo Sequencing Software

Bin Ma

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Add to Collection

Article Biochemical Research Methods

Multiplexed peptide analysis using data-independent acquisition and Skyline

Jarrett D. Egertson et al.

NATURE PROTOCOLS (2015)

Add to Collection

Article Biochemical Research Methods

Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach

Patricia de Sousa-Pereira et al.

PROTEOMICS (2015)

Add to Collection

Review Biochemistry & Molecular Biology

Mass Spectrometry-Based Detection and Assignment of Protein Posttranslational Modifications

Sophia Doll et al.

ACS CHEMICAL BIOLOGY (2015)

Add to Collection

Review Spectroscopy

MULTIPLEXED AND DATA-INDEPENDENT TANDEM MASS SPECTROMETRY FOR GLOBAL PROTEOME PROFILING

John D. Chapman et al.

MASS SPECTROMETRY REVIEWS (2014)

Add to Collection

Article Multidisciplinary Sciences

MS-GF plus makes progress towards a universal database search tool for proteomics

Sangtae Kim et al.

NATURE COMMUNICATIONS (2014)

Add to Collection

Article Biochemical Research Methods

Multiplexed MS/MS for improved data-independent acquisition

Jarrett D. Egertson et al.

NATURE METHODS (2013)

Add to Collection

Article Biochemical Research Methods

Comet: An open-source MS/MS sequence database search tool

Jimmy K. Eng et al.

PROTEOMICS (2013)

Add to Collection

Article Biochemical Research Methods

A fast SEQUEST cross correlation algorithm

Jimmy K. Eng et al.

JOURNAL OF PROTEOME RESEARCH (2008)

Add to Collection

Article Biochemical Research Methods

Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics

Thomas Koenig et al.

JOURNAL OF PROTEOME RESEARCH (2008)

Add to Collection

Article Biotechnology & Applied Microbiology

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Juergen Cox et al.

NATURE BIOTECHNOLOGY (2008)

Add to Collection

Article Biochemical Research Methods

Open mass spectrometry search algorithm

LY Geer et al.

JOURNAL OF PROTEOME RESEARCH (2004)

Add to Collection

Article Biochemical Research Methods

TANDEM: matching proteins with tandem mass spectra

R Craig et al.

BIOINFORMATICS (2004)

Add to Collection

© Peeref 2019-2024. All rights reserved.