4.3 Review

Cardiovascular proteomics in the era of big data: experimental and computational advances

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

KEGG as a reference resource for gene and protein annotation

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

The Pfam protein families database: towards a more sustainable future

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2016)

Editorial Material Cardiac & Cardiovascular Systems

Connecting the Dots From Big Data to Healthy Heart

Edward Lau et al.

CIRCULATION (2016)

Article Biochemical Research Methods

The Perseus computational platform for comprehensive analysis of (prote)omics data

Stefka Tyanova et al.

NATURE METHODS (2016)

Article Multidisciplinary Sciences

A draft map of the mouse pluripotent stem cell spatial proteome

Andy Christoforou et al.

NATURE COMMUNICATIONS (2016)

Article Mathematical & Computational Biology

HistoneDB 2.0: a histone database with variants-an integrated resource to explore histones and their variants

Eli J. Draizen et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2016)

Article Multidisciplinary Sciences

A large dataset of protein dynamics in the mammalian heart proteome

Edward Lau et al.

SCIENTIFIC DATA (2016)

Article Endocrinology & Metabolism

Removal of Abnormal Myofilament O-GlcNAcylation Restores Ca2+ Sensitivity in Diabetic Cardiac Muscle

Genaro A. Ramirez-Correa et al.

DIABETES (2015)

Article Cardiac & Cardiovascular Systems

High fat, high sucrose diet causes cardiac mitochondrial dysfunction due in part to oxidative post-translational modification of mitochondrial complex II

Aaron L. Sverdlov et al.

JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY (2015)

Review Cardiac & Cardiovascular Systems

Mitochondrial protein turnover: Methods to measure turnover rates on a large scale

X'avia C. Y. Chan et al.

JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY (2015)

Article Cardiac & Cardiovascular Systems

Characterization of the cardiac succinylome and its role in ischemia-reperfusion injury

Jennifer A. Boylston et al.

JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY (2015)

Article Biochemical Research Methods

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

T. Xu et al.

JOURNAL OF PROTEOMICS (2015)

Letter Cardiac & Cardiovascular Systems

Prioritizing Proteomics Assay Development for Clinical Translation

Maggie P. Y. Lam et al.

JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY (2015)

Article Cardiac & Cardiovascular Systems

Alterations in the Interactome of Serine/Threonine Protein Phosphatase Type-1 in Atrial Fibrillation Patients

David Y. Chiang et al.

JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY (2015)

Article Biochemical Research Methods

From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics

Mathieu Lavallee-Adam et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Article Biochemical Research Methods

The SEQUEST Family Tree

David L. Tabb

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Article Biochemical Research Methods

A Deeper Look into Comet-Implementation and Features

Jimmy K. Eng et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Article Biochemical Research Methods

Pivotal Role of Computers and Software in Mass Spectrometry - SEQUEST and 20 Years of Tandem MS Database Searching

John R. Yates

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2015)

Article Multidisciplinary Sciences

ΔF508 CFTR interactome remodelling promotes rescue of cystic fibrosis

Sandra Pankow et al.

NATURE (2015)

Letter Biotechnology & Applied Microbiology

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Marc Vaudel et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

Multiplexed peptide analysis using data-independent acquisition and Skyline

Jarrett D. Egertson et al.

NATURE PROTOCOLS (2015)

Article Biochemistry & Molecular Biology

MetaboAnalyst 3.0-making metabolomics more meaningful

Jianguo Xia et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Biochemical Research Methods

Visualization of proteomics data using R and Bioconductor

Laurent Gatto et al.

PROTEOMICS (2015)

Review Biochemical Research Methods

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

Eric W. Deutsch et al.

PROTEOMICS CLINICAL APPLICATIONS (2015)

Review Biochemistry & Molecular Biology

Mitochondrial Proteins Moonlighting in the Nucleus

Richard M. Monaghan et al.

TRENDS IN BIOCHEMICAL SCIENCES (2015)

Review Biochemistry & Molecular Biology

Data processing methods and quality control strategies for label-free LC-MS protein quantification

Marianne Sandin et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2014)

Review Biochemistry & Molecular Biology

Using R and Bioconductor for proteomics data analysis

Laurent Gatto et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2014)

Article Biochemical Research Methods

Census 2: isobaric labeling data analysis

Sung Kyu Robin Park et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

Gloria M. Sheynkman et al.

BMC GENOMICS (2014)

Article Medicine, Research & Experimental

Protein kinetic signatures of the remodeling heart following isoproterenol stimulation

Maggie P. Y. Lam et al.

JOURNAL OF CLINICAL INVESTIGATION (2014)

Article Cardiac & Cardiovascular Systems

S-nitrosylation of TRIM72 at cysteine 144 is critical for protection against oxidation-induced protein degradation and cell death

Mark J. Kohr et al.

JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY (2014)

Article Biochemical Research Methods

Characterization, Design, and Function of the Mitochondrial Proteome: From Organs to Organisms

Christopher Lotz et al.

JOURNAL OF PROTEOME RESEARCH (2014)

Article Biochemical Research Methods

MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

Viktoria Dorfer et al.

JOURNAL OF PROTEOME RESEARCH (2014)

Article Biochemical Research Methods

PSEA-Quant: A Protein Set Enrichment Analysis on Label-Free and Label-Based Protein Quantification Data

Mathieu Lavallee-Adam et al.

JOURNAL OF PROTEOME RESEARCH (2014)

Article Biochemical Research Methods

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

Sean McIlwain et al.

JOURNAL OF PROTEOME RESEARCH (2014)

Article Biochemical Research Methods

The One Hour Yeast Proteome

Alexander S. Hebert et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Article Biochemical Research Methods

Statistical Approach to Protein Quantification

Sarah Gerster et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Article Biochemical Research Methods

Combinatorial Approach for Large-scale Identification of Linked Peptides from Tandem Mass Spectrometry Spectra*

Jian Wang et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Article Biochemical Research Methods

A Foundation for Reliable Spatial Proteomics Data Analysis

Laurent Gatto et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Article Multidisciplinary Sciences

A draft map of the human proteome

Min-Sik Kim et al.

NATURE (2014)

Article Multidisciplinary Sciences

Mass-spectrometry-based draft of the human proteome

Mathias Wilhelm et al.

NATURE (2014)

Letter Biotechnology & Applied Microbiology

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

Hannes L. Roest et al.

NATURE BIOTECHNOLOGY (2014)

Article Multidisciplinary Sciences

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

Sangtae Kim et al.

NATURE COMMUNICATIONS (2014)

Editorial Material Cardiac & Cardiovascular Systems

Cyclophilin D and Acetylation A New Link in Cardiac Signaling

Maggie P. Y. Lam et al.

CIRCULATION RESEARCH (2013)

Article Cardiac & Cardiovascular Systems

Cyclophilin D Modulates Mitochondrial Acetylome

Tiffany Tuyen M. Nguyen et al.

CIRCULATION RESEARCH (2013)

Article Cardiac & Cardiovascular Systems

Integration of Cardiac Proteome Biology and Medicine by a Specialized Knowledgebase

Nobel C. Zong et al.

CIRCULATION RESEARCH (2013)

Article Biochemical Research Methods

Modified MuDPIT Separation Identified 4488 Proteins in a System-wide Analysis of Quiescence in Yeast

Kristofor J. Webb et al.

JOURNAL OF PROTEOME RESEARCH (2013)

Article Biochemical Research Methods

Expanding Tandem Mass Spectral Libraries of Phosphorylated Peptides: Advances and Applications

Yingwei Hu et al.

JOURNAL OF PROTEOME RESEARCH (2013)

Article Biochemical Research Methods

A novel spectral library workflow to enhance protein identifications

Haomin Li et al.

JOURNAL OF PROTEOMICS (2013)

Article Biochemical Research Methods

Pyteomics-a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

Anton A. Goloborodko et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2013)

Article Biochemical Research Methods

Digestion and depletion of abundant proteins improves proteomic coverage

Bryan R. Fonslow et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

Dattatreya Mellacheruvu et al.

NATURE METHODS (2013)

Article Biochemistry & Molecular Biology

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

Jing Wang et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemical Research Methods

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

Jimmy K. Eng et al.

PROTEOMICS (2013)

Review Cardiac & Cardiovascular Systems

Good Enough Solutions and the Genetics of Complex Diseases

James N. Weiss et al.

CIRCULATION RESEARCH (2012)

Article Biochemical Research Methods

Topograph, a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements

Edward J. Hsieh et al.

MOLECULAR & CELLULAR PROTEOMICS (2012)

Article Biochemical Research Methods

Metabolic Labeling Reveals Proteome Dynamics of Mouse Mitochondria

Tae-Young Kim et al.

MOLECULAR & CELLULAR PROTEOMICS (2012)

Review Biochemical Research Methods

Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions

Paola Picotti et al.

NATURE METHODS (2012)

Review Cardiac & Cardiovascular Systems

Overview The Maturing of Proteomics in Cardiovascular Research

Jennifer E. Van Eyk

CIRCULATION RESEARCH (2011)

Article Biochemical Research Methods

MSblender: A Probabilistic Approach for Integrating Peptide Identifications from Multiple Database Search Engines

Taejoon Kwon et al.

JOURNAL OF PROTEOME RESEARCH (2011)

Article Biochemical Research Methods

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

Juergen Cox et al.

JOURNAL OF PROTEOME RESEARCH (2011)

Article Multidisciplinary Sciences

SUMO1-dependent modulation of SERCA2a in heart failure

Changwon Kho et al.

NATURE (2011)

Article Biochemical Research Methods

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

Ari M. Frank et al.

NATURE METHODS (2011)

Review Biochemical Research Methods

Role of spectral counting in quantitative proteomics

Deborah H. Lundgren et al.

EXPERT REVIEW OF PROTEOMICS (2010)

Article Biochemical Research Methods

Super-SILAC mix for quantitative proteomics of human tumor tissue

Tamar Geiger et al.

NATURE METHODS (2010)

Review Biochemical Research Methods

A guided tour of the Trans-Proteomic Pipeline

Eric W. Deutsch et al.

PROTEOMICS (2010)

Article Biochemical Research Methods

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Da Wei Huang et al.

NATURE PROTOCOLS (2009)

Article Biochemical Research Methods

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

Aaron A. Klammer et al.

BIOINFORMATICS (2008)

Article Biochemical Research Methods

OpenMS-An open-source software framework for mass spectrometry

Marc Sturm et al.

BMC BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

A mitochondrial protein compendium elucidates complex I disease biology

David J. Pagliarini et al.

Article Biochemical Research Methods

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Lukas Kall et al.

NATURE METHODS (2007)

Review Cardiac & Cardiovascular Systems

Proteomics of the heart - Unraveling disease

E McGregor et al.

CIRCULATION RESEARCH (2006)

Article Biochemical Research Methods

TANDEM: matching proteins with tandem mass spectra

R Craig et al.

BIOINFORMATICS (2004)

Article Biochemical Research Methods

Phosphosite: A bioinformatics resource dedicated to physiological protein phosphorylation

PV Hornbeck et al.

PROTEOMICS (2004)

Article Chemistry, Analytical

A statistical model for identifying proteins by tandem mass spectrometry

AI Nesvizhskii et al.

ANALYTICAL CHEMISTRY (2003)

Article Cardiac & Cardiovascular Systems

Proteomics in cardiovascular biology and medicine

J Loscalzo

CIRCULATION (2003)

Article Biotechnology & Applied Microbiology

Large-scale analysis of the yeast proteome by multidimensional protein identification technology

MP Washburn et al.

NATURE BIOTECHNOLOGY (2001)