Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides
出版年份 2021 全文链接
标题
Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides
作者
关键词
-
出版物
PROTEOMICS
Volume -, Issue -, Pages 2100008
出版商
Wiley
发表日期
2021-06-19
DOI
10.1002/pmic.202100008
参考文献
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。- Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions
- (2021) Chaitanya Erady et al. npj Genomic Medicine
- Recent advances in mass spectrometry–based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions
- (2021) Bertrand Fabre et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins
- (2021) Dörte Schlesinger et al. FEBS Journal
- Reprograming of sRNA target specificity by the leader peptide peTrpL in response to antibiotic exposure
- (2021) Hendrik Melior et al. NUCLEIC ACIDS RESEARCH
- Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
- (2021) Hannes Petruschke et al. Microbiome
- The largely unexplored biology of small proteins in pro‐ and eukaryotes
- (2021) Ruth Steinberg et al. FEBS Journal
- Multi-protease Approach for the Improved Identification and Molecular Characterization of Small Proteins and Short Open Reading Frame-Encoded Peptides
- (2021) Philipp T. Kaulich et al. JOURNAL OF PROTEOME RESEARCH
- A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype–Proteotype–Phenotype Relationships
- (2020) Adithi R. Varadarajan et al. JOURNAL OF PROTEOME RESEARCH
- Pervasive functional translation of noncanonical human open reading frames
- (2020) Jin Chen et al. SCIENCE
- Comparative proteomic profiling of unannotated microproteins and alternative proteins in human cell lines
- (2020) Xiongwen Cao et al. JOURNAL OF PROTEOME RESEARCH
- Large-scale Discovery of Non-conventional Peptides in Maize and Arabidopsis Through an Integrated Peptidogenomic Pipeline
- (2020) Shunxi Wang et al. Molecular Plant
- Complementarity of Different SDS‐PAGE Gel Staining Methods for the Identification of Short Open Reading Frame‐encoded Peptides
- (2020) Philipp T. Kaulich et al. PROTEOMICS
- The NBDY Microprotein Regulates Cellular RNA Decapping
- (2020) Zhenkun Na et al. BIOCHEMISTRY
- Optimized Proteomics Workflow for the Detection of Small Proteins
- (2020) Jürgen Bartel et al. JOURNAL OF PROTEOME RESEARCH
- The FUS gene is dual‐coding with both proteins contributing to FUS ‐mediated toxicity
- (2020) Marie A Brunet et al. EMBO REPORTS
- Multidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame-encoded peptides in top-down proteomics
- (2020) Liam Cassidy et al. Journal of Proteomics
- Identification and analysis of small proteins and short open reading frame encoded peptides in Hep3B cell
- (2020) Bing Wang et al. Journal of Proteomics
- Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis
- (2020) Shannon L. Thomas et al. JOURNAL OF SEPARATION SCIENCE
- Small but Smart: On the Diverse Role of Small Proteins in the Regulation of Cyanobacterial Metabolism
- (2020) Fabian Brandenburg et al. Life-Basel
- Shedding Light on the Ghost Proteome
- (2020) Tristan Cardon et al. TRENDS IN BIOCHEMICAL SCIENCES
- PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations
- (2019) Bo Wen et al. GENOME RESEARCH
- Depletion of High-Molecular-Mass Proteins for the Identification of Small Proteins and Short Open Reading Frame Encoded Peptides in Cellular Proteomes
- (2019) Liam Cassidy et al. JOURNAL OF PROTEOME RESEARCH
- Nuclei of HeLa cells interactomes unravel a network of ghost proteins involved in proteins translation
- (2019) Tristan Cardon et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Small-protein enrichment assay enables the rapid, unbiased analysis of over 100 low abundance factors from human plasma
- (2019) Dylan Harney et al. MOLECULAR & CELLULAR PROTEOMICS
- Online Comprehensive High pH Reversed Phase × Low pH Reversed Phase Approach for Two-Dimensional Separations of Intact Proteins in Top-Down Proteomics
- (2019) Yehia Z. Baghdady et al. ANALYTICAL CHEMISTRY
- Alternative ORFs and small ORFs: shedding light on the dark proteome
- (2019) Mona Wu Orr et al. NUCLEIC ACIDS RESEARCH
- Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins
- (2019) Tristan Cardon et al. ANALYTICAL CHEMISTRY
- Enrichment and identification of small proteins in a simplified human gut microbiome
- (2019) Hannes Petruschke et al. Journal of Proteomics
- Enrichment-Based Proteogenomics Identifies Microproteins, Missing Proteins, and Novel smORFs in Saccharomyces cerevisiae
- (2018) Cuitong He et al. JOURNAL OF PROTEOME RESEARCH
- Efficient and robust proteome-wide approaches for cross-linking mass spectrometry
- (2018) Oleg Klykov et al. Nature Protocols
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
- (2017) Ulrich Omasits et al. GENOME RESEARCH
- Gentle Introduction to the Statistical Foundations of False Discovery Rate in Quantitative Proteomics
- (2017) Thomas Burger JOURNAL OF PROTEOME RESEARCH
- Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli
- (2017) Nadia G. D’Lima et al. JOURNAL OF PROTEOME RESEARCH
- Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation
- (2017) Nicholas M. Riley et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- Classification and function of small open reading frames
- (2017) Juan-Pablo Couso et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Separation and identification of mouse brain tissue microproteins using top-down method with high resolution nanocapillary liquid chromatography mass spectrometry
- (2017) Wenxue Li et al. PROTEOMICS
- Biologically active peptides encoded by small open reading frames
- (2017) R. A. Khazigaleeva et al. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY
- Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins
- (2017) Sondos Samandi et al. eLife
- Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides
- (2016) Jiao Ma et al. ANALYTICAL CHEMISTRY
- Progress in Top-Down Proteomics and the Analysis of Proteoforms
- (2016) Timothy K. Toby et al. Annual Review of Analytical Chemistry
- Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei
- (2016) Liam Cassidy et al. JOURNAL OF PROTEOME RESEARCH
- Tandem mass spectral libraries of peptides and their roles in proteomics research
- (2016) Wenguang Shao et al. MASS SPECTROMETRY REVIEWS
- Coming of age: ten years of next-generation sequencing technologies
- (2016) Sara Goodwin et al. NATURE REVIEWS GENETICS
- Spectral library searching in proteomics
- (2016) Johannes Griss PROTEOMICS
- Common errors in mass spectrometry-based analysis of post-translational modifications
- (2016) Min-Sik Kim et al. PROTEOMICS
- Identification and validation of novel small proteins inPseudomonas putida
- (2016) Xiaochen Yang et al. Environmental Microbiology Reports
- Ribosomal profiling adds new coding sequences to the proteome
- (2015) M. A. S. Mumtaz et al. BIOCHEMICAL SOCIETY TRANSACTIONS
- First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1
- (2015) Daniela Prasse et al. BIOCHIMIE
- A note on the false discovery rate of novel peptides in proteogenomics
- (2015) Kun Zhang et al. BIOINFORMATICS
- Proteomics beyond trypsin
- (2015) Liana Tsiatsiani et al. FEBS Journal
- Is isolation of comprehensive human plasma peptidomes an achievable quest?
- (2015) S. Mahboob et al. Journal of Proteomics
- Unexpected features of the dark proteome
- (2015) Nelson Perdigão et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- IPeak: An open source tool to combine results from multiple MS/MS search engines
- (2015) Bo Wen et al. PROTEOMICS
- Current approaches and challenges in targeted absolute quantification of membrane proteins
- (2015) Christian Trötschel et al. PROTEOMICS
- Current peptidomics: Applications, purification, identification, quantification, and functional analysis
- (2015) David C. Dallas et al. PROTEOMICS
- Small Proteins Can No Longer Be Ignored
- (2014) Gisela Storz et al. Annual Review of Biochemistry
- Top Down proteomics: Facts and perspectives
- (2014) Adam D. Catherman et al. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
- Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue
- (2014) Jiao Ma et al. JOURNAL OF PROTEOME RESEARCH
- Proteogenomics: concepts, applications and computational strategies
- (2014) Alexey I Nesvizhskii NATURE METHODS
- Emerging evidence for functional peptides encoded by short open reading frames
- (2014) Shea J. Andrews et al. NATURE REVIEWS GENETICS
- Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis
- (2014) Alexandre Zougman et al. PROTEOMICS
- Maximizing recovery of water-soluble proteins through acetone precipitation
- (2013) Andrew M.J. Crowell et al. ANALYTICA CHIMICA ACTA
- Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames
- (2013) Adam G. Schwaid et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Deep Coverage of theEscherichia coliProteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments
- (2013) Karsten Krug et al. MOLECULAR & CELLULAR PROTEOMICS
- Proteoform: a single term describing protein complexity
- (2013) Lloyd M Smith et al. NATURE METHODS
- SAINT-MS1: Protein–Protein Interaction Scoring Using Label-free Intensity Data in Affinity Purification-Mass Spectrometry Experiments
- (2012) Hyungwon Choi et al. JOURNAL OF PROTEOME RESEARCH
- Peptidomic discovery of short open reading frame–encoded peptides in human cells
- (2012) Sarah A Slavoff et al. Nature Chemical Biology
- Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance
- (2012) E. C. Hobbs et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- An expanding universe of small proteins
- (2011) Errett C Hobbs et al. CURRENT OPINION IN MICROBIOLOGY
- Sample Preparation Techniques for the Untargeted LC-MS-Based Discovery of Peptides in Complex Biological Matrices
- (2011) Inez Finoulst et al. JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY
- Optimization of parameters for coverage of low molecular weight proteins
- (2010) Stephan A. Müller et al. ANALYTICAL AND BIOANALYTICAL CHEMISTRY
- Identification of a chloroform-soluble membrane miniprotein in Escherichia coli and its homolog in Salmonella typhimurium
- (2010) Ziqiang Guan et al. ANALYTICAL BIOCHEMISTRY
- High-Yield Peptide-Extraction Method for the Discovery of Subnanomolar Biomarkers from Small Serum Samples
- (2010) Yusuke Kawashima et al. JOURNAL OF PROTEOME RESEARCH
- A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
- (2010) Alexey I. Nesvizhskii Journal of Proteomics
- Expanding the Dipeptidyl Peptidase 4-Regulated Peptidome via an Optimized Peptidomics Platform
- (2010) Arthur D. Tinoco et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- PeptideClassifier for protein inference and targeted quantitative proteomics
- (2010) Ermir Qeli et al. NATURE BIOTECHNOLOGY
- Small Stress Response Proteins in Escherichia coli: Proteins Missed by Classical Proteomic Studies
- (2009) M. R. Hemm et al. JOURNAL OF BACTERIOLOGY
- A centrifugal ultrafiltration strategy for isolating the low-molecular weight (≤25K) component of human plasma proteome
- (2009) David W. Greening et al. Journal of Proteomics
- Top-down proteomics reveals novel protein forms expressed in methanosarcina acetivorans
- (2009) Jonathan T. Ferguson et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- Quantitative peptidomics reveal brain peptide signatures of behavior
- (2009) A. Brockmann et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
- (2009) N. T. Ingolia et al. SCIENCE
- A 2D reversed-phase × ion-pair reversed-phase HPLC-MALDI TOF/TOF-MS approach for shotgun proteome analysis
- (2008) Maria Lasaosa et al. ANALYTICAL AND BIOANALYTICAL CHEMISTRY
- Gel-Eluted Liquid Fraction Entrapment Electrophoresis: An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation
- (2008) John C. Tran et al. ANALYTICAL CHEMISTRY
- Alternative translation start sites and hidden coding potential of eukaryotic mRNAs
- (2008) Alex V. Kochetov BIOESSAYS
- Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies
- (2008) Brian C. Searle et al. JOURNAL OF PROTEOME RESEARCH
- Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
- (2008) Marcel E. Dinger et al. PLoS Computational Biology
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started