PeptideAtlas
Names
More detailed information about this field from each metasource.
PeptideAtlas
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
PeptideAtlas peptide database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:53.805279
peptideatlas
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:53.805279
Names
More detailed information about this field from each metasource.
PeptideAtlas
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
PeptideAtlas peptide database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:53.805279
peptideatlas
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:53.805279
Other names: PeptideAtlas peptide database, peptideatlas
Names
More detailed information about this field from each metasource.
PeptideAtlas
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
PeptideAtlas peptide database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:53.805279
peptideatlas
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:53.805279
The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and sequence and spectral library searches are applied. Analyses are performed to produce a probability of correct identification for all results in a uniform manner, together with false discovery rates at the whole-atlas level.
Description
More detailed information about this field from each metasource.
The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and sequence and spectral library searches are applied. Analyses are performed to produce a probability of correct identification for all results in a uniform manner, together with false discovery rates at the whole-atlas level.
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
The PeptideAtlas (1) is a multi-organism, publicly accessible compendium of peptides identified in a large set of LC-MS/MS proteomics experiments. Some of the experimental data have been already published; many are still unpublished. All results of sequence searching have subsequently been processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner to insure a high quality database. All peptides have been mapped to Ensembl and can be viewed as custom tracks on the Ensembl Genome Browser. The PeptideAtlas will continue to grow as more datasets and organisms are added. We welcome data submissions, which we will incorporate into the atlas.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The PeptideAtlas validates expressed proteins to provide eukaryotic genome data. Peptide Atlas provides data to advance biological discoveries in humans. The PeptideAtlas accepts proteomic data from high-throughput processes and encourages data submission.
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
A multi-organism compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:53.805279
Webpage:
http://www.peptideatlas.orgWebpage
More detailed information about this field from each metasource.
http://www.peptideatlas.org
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:53.805279
http://www.peptideatlas.org/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
Licence:
Name: Peptide Atlas Availability StatementLicence name
More detailed information about this field from each metasource.
Peptide Atlas Availability Statement
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Public Domain
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
Licence URL
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http://www.peptideatlas.org/public/faq.php
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://www.peptideatlas.org/overview.php
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
The PeptideAtlas project
PMID: 16381952
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
PMID: 18451766
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkj040
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:53.805279
Publications
More detailed information about this field from each metasource.
The PeptideAtlas project
PMID: 16381952
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
PMID: 18451766
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkj040
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:53.805279
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The PeptideAtlas project
PubMed citations: 300.
300 articles citing: The PeptideAtlas project
Multi-Omics Interdisciplinary Research Integration to Accelerate Dementia Biomarker Development (MIRIADE). PMID:35903119
Quantitative Detection of Protein Splice Variants by Selected Reaction Monitoring (SRM) Mass Spectrometry. PMID:35895268
Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT-474 breast cancer cell line. PMID:35568821
Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. PMID:35532924
Data-Independent Acquisition Enables Robust Quantification of 400 Proteins in Non-Depleted Canine Plasma. PMID:35324581
Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. PMID:35216306
Alteration of EIF2 Signaling, Glycolysis, and Dopamine Secretion in Form-Deprived Myopia in Response to 1% Atropine Treatment: Evidence From Interactive iTRAQ-MS and SWATH-MS Proteomics Using a Guinea Pig Model. PMID:35153787
An adipose lncRAP2-Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs. PMID:35036870
Physical Interactions With Bacteria and Protozoan Parasites Establish the Scavenger Receptor SSC4D as a Broad-Spectrum Pattern Recognition Receptor. PMID:35003072
Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline. PMID:34919405
Immunoinformatics-Based Designing of a Multi-Epitope Chimeric Vaccine From Multi-Domain Outer Surface Antigens of Leptospira. PMID:34917072
Biochemical Characterisation of Human Transglutaminase 4. PMID:34830327
NGAL as a Potential Target in Tumor Microenvironment. PMID:34830212
Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses. PMID:34740240
Identification of Endothelial Proteins in Plasma Associated With Cardiovascular Risk Factors. PMID:34706560
An Introduction to Advanced Targeted Acquisition Methods. PMID:34673283
Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. PMID:34670092
Mapping Sphingolipid Metabolism Pathways during Phagosomal Maturation. PMID:34647453
AlphaMap: an open-source python package for the visual annotation of proteomics data with sequence specific knowledge. PMID:34586352
Endothelial Heparan Sulfate Mediates Hepatic Neutrophil Trafficking and Injury during Staphylococcus aureus Sepsis. PMID:34544271
Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories. PMID:34361974
Identification of Novel Rotihibin Analogues in Streptomyces scabies, Including Discovery of Its Biosynthetic Gene Cluster. PMID:34346752
ppx: Programmatic Access to Proteomics Data Repositories. PMID:34342226
On the feasibility of deep learning applications using raw mass spectrometry data. PMID:34252933
Software Options for the Analysis of MS-Proteomic Data. PMID:34236654
Universal Spectrum Identifier for mass spectra. PMID:34183830
Development of Parallel Reaction Monitoring Assays for the Detection of Aggressive Prostate Cancer Using Urinary Glycoproteins. PMID:34106707
Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data. PMID:34100982
Comprehensive Phosphoproteomic Analysis of Nostoc flagelliforme in Response to Dehydration Provides Insights into Plant ROS Signaling Transduction. PMID:34095650
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data. PMID:33950201
Protein interactome of the Cancerous Inhibitor of protein phosphatase 2A (CIP2A) in Th17 cells. PMID:33817627
CIDer: A Statistical Framework for Interpreting Differences in CID and HCD Fragmentation. PMID:33729787
Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease. PMID:33480174
Structural and functional comparison of SARS-CoV-2-spike receptor binding domain produced in Pichia pastoris and mammalian cells. PMID:33311634
Shotgun proteomics coupled to nanoparticle-based biomarker enrichment reveals a novel panel of extracellular matrix proteins as candidate serum protein biomarkers for early-stage breast cancer detection. PMID:33267867
Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid. PMID:33252673
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
Cell type-selective secretome profiling in vivo. PMID:33199915
Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. PMID:33166149
SARS-CoV-2 evades immune detection in alveolar macrophages. PMID:33112036
Mass Spectrometry Supports That the Structure of Circulating Human Insulin-Like Factor 3 Is a Heterodimer. PMID:32982964
FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs. PMID:32977531
Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF. PMID:32958672
StoneMod: a database for kidney stone modulatory proteins with experimental evidence. PMID:32934277
Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality. PMID:32737166
A comprehensive investigation of the mRNA and protein level of ACE2, the putative receptor of SARS-CoV-2, in human tissues and blood cells. PMID:32669955
Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context. PMID:32669370
Pathological Conversion of Mouse Perivascular Adipose Tissue by Notch Activation. PMID:32640901
Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signalling networks using SILAC-based phosphoproteomics. PMID:32501498
Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries. PMID:32312845
Integrative Modeling of a Sin3/HDAC Complex Sub-structure. PMID:32294434
Multiplexed MRM-based protein quantification of putative prognostic biomarkers for chronic kidney disease progression in plasma. PMID:32179759
Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. PMID:32138667
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
In-Depth Mapping of the Urinary N-Glycoproteome: Distinct Signatures of ccRCC-related Progression. PMID:31963743
Optimization of TripleTOF spectral simulation and library searching for confident localization of phosphorylation sites. PMID:31790495
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. PMID:31599596
Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. PMID:31573204
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. PMID:31537640
Cellular Interactions in the Tumor Microenvironment: The Role of Secretome. PMID:31528221
High-Throughput Assessment of Kinome-wide Activation States. PMID:31521607
N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. PMID:31516400
A de novo evolved gene in the house mouse regulates female pregnancy cycles. PMID:31436535
Quantifying the impact of public omics data. PMID:31383865
In vivo proteomics identifies the competence regulon and AliB oligopeptide transporter as pathogenic factors in pneumococcal meningitis. PMID:31356624
C-terminal proteolysis of the collagen VI α3 chain by BMP-1 and proprotein convertase(s) releases endotrophin in fragments of different sizes. PMID:31346034
Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results. PMID:31260318
Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses. PMID:31253788
A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies. PMID:31227708
Pixel: a content management platform for quantitative omics data. PMID:30944779
Proteomic discovery of substrates of the cardiovascular protease ADAMTS7. PMID:30926607
Asymmetric distribution of glucose transporter mRNA provides a growth advantage in yeast. PMID:30910878
Intelligence Algorithms for Protein Classification by Mass Spectrometry. PMID:30534555
Targeting LINC00673 expression triggers cellular senescence in lung cancer. PMID:30499379
Artificial Intelligence Understands Peptide Observability and Assists With Absolute Protein Quantification. PMID:30483279
Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion. PMID:30346791
Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the neXt-MP50 Challenge. PMID:30280577
Expanding the Use of Spectral Libraries in Proteomics. PMID:30270626
Iron in Friedreich Ataxia: A Central Role in the Pathophysiology or an Epiphenomenon? PMID:30235822
Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper. PMID:30230343
Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. PMID:30207828
PDV: an integrative proteomics data viewer. PMID:30169737
Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra. PMID:30096983
Cleavage of Peptides from Amphibian Skin Revealed by Combining Analysis of Gland Secretion and in Situ MALDI Imaging Mass Spectrometry. PMID:30023919
Loose ends: almost one in five human genes still have unresolved coding status. PMID:29982784
Endogenous Cell Type-Specific Disrupted in Schizophrenia 1 Interactomes Reveal Protein Networks Associated With Neurodevelopmental Disorders. PMID:29961565
Understanding Leishmania parasites through proteomics and implications for the clinic. PMID:29717934
Quantitative targeted proteomic analysis of potential markers of tyrosine kinase inhibitor (TKI) sensitivity in EGFR mutated lung adenocarcinoma. PMID:29660496
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules. PMID:29657133
Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. PMID:29626081
A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry. PMID:29599190
Protein S-Nitrosylation Controls Glycogen Synthase Kinase 3β Function Independent of Its Phosphorylation State. PMID:29563102
A comprehensive catalog of predicted functional upstream open reading frames in humans. PMID:29562350
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction. PMID:29409446
Multi-field query expansion is effective for biomedical dataset retrieval. PMID:29220457
Selected reaction monitoring approach for validating peptide biomarkers. PMID:29203663
MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting. PMID:29192002
ProteomicsDB. PMID:29106664
Acetylome Profiling Reveals Extensive Lysine Acetylation of the Fatty Acid Metabolism Pathway in the Diatom Phaeodactylum tricornutum. PMID:29093020
The SysteMHC Atlas project. PMID:28985418
Targeted proteomics reveals promising biomarkers of disease activity and organ involvement in antineutrophil cytoplasmic antibody-associated vasculitis. PMID:28962592
The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. PMID:28938075
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. PMID:28849660
Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes. PMID:28837811
Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins. PMID:28808993
NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity. PMID:28775335
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. PMID:28691345
A comprehensive analysis and annotation of human normal urinary proteome. PMID:28596590
Lysine Acetylome Analysis Reveals Photosystem II Manganese-stabilizing Protein Acetylation is Involved in Negative Regulation of Oxygen Evolution in Model Cyanobacterium Synechococcus sp. PCC 7002. PMID:28550166
The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. PMID:28536419
Last rolls of the yoyo: Assessing the human canonical protein count. PMID:28529709
CancerPDF: A repository of cancer-associated peptidome found in human biofluids. PMID:28473704
The Proteins API: accessing key integrated protein and genome information. PMID:28383659
Cervical Cancer Cell Line Secretome Highlights the Roles of Transforming Growth Factor-Beta-Induced Protein ig-h3, Peroxiredoxin-2, and NRF2 on Cervical Carcinogenesis. PMID:28261610
"Omics"-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives. PMID:28248238
Global Post-Translational Modification Discovery. PMID:28248113
Correlation of pre-operative plasma protein concentrations in cardiac surgery patients with bleeding outcomes using a targeted quantitative proteomics approach. PMID:28176468
The PeptideAtlas of the Domestic Laying Hen. PMID:28166638
Identifying the missing proteins in human proteome by biological language model. PMID:28155671
Protein Bioinformatics Databases and Resources. PMID:28150231
Targeted Proteomics for Multiplexed Verification of Markers of Colorectal Tumorigenesis. PMID:28062797
A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. PMID:27918579
ZFAS1: a long noncoding RNA associated with ribosomes in breast cancer cells. PMID:27871336
Systems Medicine as an Emerging Tool for Cardiovascular Genetics. PMID:27626034
Rational engineering of a virulence gene from Mycobacterium tuberculosis facilitates proteomic analysis of a natural protein N-terminus. PMID:27625110
TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions. PMID:27609421
Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry. PMID:27606673
Data sources for in vivo molecular profiling of human phenotypes. PMID:27599755
N-Terminal Peptide Detection with Optimized Peptide-Spectrum Matching and Streamlined Sequence Libraries. PMID:27498768
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. PMID:27493588
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1. PMID:27490519
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. PMID:27479329
Computational studies of human class V alcohol dehydrogenase - the odd sibling. PMID:27455956
Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. PMID:27356587
PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq. PMID:27316337
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow. PMID:27250503
Current state of the art for enhancing urine biomarker discovery. PMID:27232439
Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila. PMID:27189981
The UniProtKB guide to the human proteome. PMID:26896845
Supernatant protein biomarkers of red blood cell storage hemolysis as determined through an absolute quantification proteomics technology. PMID:26813021
The 5300-year-old Helicobacter pylori genome of the Iceman. PMID:26744403
An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64. PMID:26618079
The UCSC Genome Browser database: 2016 update. PMID:26590259
Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver. PMID:26582562
Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics. PMID:26569054
A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage. PMID:26493587
Neurodegeneration and Cancer: Where the Disorder Prevails. PMID:26493371
Proteomic analysis of naturally-sourced biological scaffolds. PMID:26476196
Exploring the potential of public proteomics data. PMID:26449181
Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer. PMID:26423119
Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search. PMID:26418581
Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification. PMID:26325288
Targeted Proteomics to Assess the Response to Anti-Angiogenic Treatment in Human Glioblastoma (GBM). PMID:26243272
MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. PMID:26204236
Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. PMID:26193931
Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates. PMID:26177073
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PMID:26061177
Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. PMID:25884379
Quantitative proteogenomic profiling of epidermal barrier formation in vitro. PMID:25862149
Quantitative proteome analysis of temporally resolved phagosomes following uptake via key phagocytic receptors. PMID:25755298
Proteins interacting with cloning scars: a source of false positive protein-protein interactions. PMID:25704442
Proteogenomic analysis and global discovery of posttranslational modifications in prokaryotes. PMID:25512518
Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA). PMID:25473088
The UCSC Genome Browser database: 2015 update. PMID:25428374
Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites. PMID:25405079
Beyond protein expression, MOPED goes multi-omics. PMID:25404128
Decoding neuroproteomics: integrating the genome, translatome and functional anatomy. PMID:25349915
Identifying novel biomarkers through data mining-a realistic scenario? PMID:25347964
Mass spectrometry assays of plasma biomarkers to predict radiographic progression of knee osteoarthritis. PMID:25287745
Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. PMID:25265570
PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species. PMID:25228907
Acetylome analysis reveals diverse functions of lysine acetylation in Mycobacterium tuberculosis. PMID:25180227
Cracking the ANP32 whips: important functions, unequal requirement, and hints at disease implications. PMID:25156960
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations. PMID:25149441
Expediting SRM assay development for large-scale targeted proteomics experiments. PMID:25145539
Correlation of phenotypic profiles using targeted proteomics identifies mycobacterial esx-1 substrates. PMID:25106450
Drafts of the human proteome. PMID:25101745
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. PMID:25089180
Cloning and characterization of a novel Drosophila stress induced DNase. PMID:25083901
Analyzing the first drafts of the human proteome. PMID:25014353
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. PMID:24939129
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
PIQMIe: a web server for semi-quantitative proteomics data management and analysis. PMID:24861615
Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. PMID:24696503
Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development. PMID:24626130
Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics. PMID:24623587
Adenovirus composition, proteolysis, and disassembly studied by in-depth qualitative and quantitative proteomics. PMID:24591515
LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism. PMID:24555535
Quantitation of human metallothionein isoforms: a family of small, highly conserved, cysteine-rich proteins. PMID:24493013
MOPED enables discoveries through consistently processed proteomics data. PMID:24350770
Computational prediction of human salivary proteins from blood circulation and application to diagnostic biomarker identification. PMID:24324552
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. PMID:24261998
Involvement of mitochondrial dynamics in the segregation of mitochondrial matrix proteins during stationary phase mitophagy. PMID:24240771
Mass spectrometric protein maps for biomarker discovery and clinical research. PMID:24138574
The Human Genome Project: big science transforms biology and medicine. PMID:24040834
Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans. PMID:24002365
Integration of cardiac proteome biology and medicine by a specialized knowledgebase. PMID:23965338
A fast Peptide Match service for UniProt Knowledgebase. PMID:23958731
Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PMID:23950983
Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet. PMID:23860498
A Candida albicans PeptideAtlas. PMID:23811049
Review of software tools for design and analysis of large scale MRM proteomic datasets. PMID:23702368
Oncogenic H-ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition. PMID:23645497
Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. PMID:23629695
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. PMID:23599424
Global remodelling of cellular microenvironment due to loss of collagen VII. PMID:23591773
Glycocapture-assisted global quantitative proteomics (gagQP) reveals multiorgan responses in serum toxicoproteome. PMID:23540550
Rearrangements within human spliceosomes captured after exon ligation. PMID:23345524
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. PMID:23334424
Chapter 2: Data-driven view of disease biology. PMID:23300408
Context-sensitive markov models for peptide scoring and identification from tandem mass spectrometry. PMID:23289783
Yeast protein phosphatase 2A-Cdc55 regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 chromatin recruitment. PMID:23275436
A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. PMID:23259914
The state of the human proteome in 2012 as viewed through PeptideAtlas. PMID:23215161
A quantitative proteomic profile of the Nrf2-mediated antioxidant response of macrophages to oxidized LDL determined by multiplexed selected reaction monitoring. PMID:23166812
APPRIS: annotation of principal and alternative splice isoforms. PMID:23161672
Current algorithmic solutions for peptide-based proteomics data generation and identification. PMID:23142544
GENCODE: the reference human genome annotation for The ENCODE Project. PMID:22955987
Interfaces to PeptideAtlas: a case study of standard data access systems. PMID:22941959
Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. PMID:22865924
A Bovine PeptideAtlas of milk and mammary gland proteomes. PMID:22837157
Parasites, proteomes and systems: has Descartes' clock run out of time? PMID:22828391
Quantitative multiple reaction monitoring of peptide abundance introduced via a capillary zone electrophoresis-electrospray interface. PMID:22690842
Automated selected reaction monitoring software for accurate label-free protein quantification. PMID:22658081
Direct detection of bacterial protein secretion using whole colony proteomics. PMID:22580590
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. PMID:22577014
Methods for visual mining of genomic and proteomic data atlases. PMID:22524279
Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator. PMID:22493177
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. PMID:22446687
The mzIdentML data standard for mass spectrometry-based proteomics results. PMID:22375074
Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs. PMID:22373085
Targeted proteomics of the eicosanoid biosynthetic pathway completes an integrated genomics-proteomics-metabolomics picture of cellular metabolism. PMID:22361236
PASSEL: the PeptideAtlas SRMexperiment library. PMID:22318887
Analysis of high accuracy, quantitative proteomics data in the MaxQB database. PMID:22301388
Mining PeptideAtlas for biomarkers and therapeutics in human disease. PMID:22236120
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions. PMID:21967198
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. PMID:21867535
Absolute quantification of microbial proteomes at different states by directed mass spectrometry. PMID:21772258
The human proteome project: current state and future direction. PMID:21742803
A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues. PMID:21639908
Fast parallel tandem mass spectral library searching using GPU hardware acceleration. PMID:21545112
A mighty small heart: the cardiac proteome of adult Drosophila melanogaster. PMID:21541028
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. PMID:21460061
In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry. PMID:21447707
A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics. PMID:21443781
Initial characterization of the human central proteome. PMID:21269460
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. PMID:21172049
A large-scale electrophoresis- and chromatography-based determination of gene expression profiles in bovine brain capillary endothelial cells after the re-induction of blood-brain barrier properties. PMID:21078152
Integrative systems biology for data-driven knowledge discovery. PMID:21044756
The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline. PMID:20976028
Generating and navigating proteome maps using mass spectrometry. PMID:20944666
Mass spectrometry in high-throughput proteomics: ready for the big time. PMID:20805795
Two-phase Filtering Strategy for Efficient Peptide Identification from Mass Spectrometry. PMID:20717493
mzML--a community standard for mass spectrometry data. PMID:20716697
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. PMID:20677327
Recent developments in quantitative proteomics. PMID:20620221
Proteomics of plant pathogenic fungi. PMID:20589070
Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information. PMID:20585472
mspecLINE: bridging knowledge of human disease with the proteome. PMID:20219133
Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays. PMID:20171116
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. PMID:20147306
The PeptideAtlas Project. PMID:20013378
Proteomics data repositories. PMID:19795424
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. PMID:19684113
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. PMID:19606093
Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. PMID:19603825
Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. PMID:19326923
Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. PMID:19279071
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. PMID:19253293
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. PMID:19210778
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. PMID:19193216
Proteomics studies confirm the presence of alternative protein isoforms on a large scale. PMID:19017398
Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory? PMID:18957555
MAPU 2.0: high-accuracy proteomes mapped to genomes. PMID:18948283
mspire: mass spectrometry proteomics in Ruby. PMID:18930952
Selected reaction monitoring for quantitative proteomics: a tutorial. PMID:18854821
Building consensus spectral libraries for peptide identification in proteomics. PMID:18806791
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. PMID:18653799
Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. PMID:18652504
Discovering oxysterols in plasma: a window on the metabolome. PMID:18605750
Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains. PMID:18560578
A mouse plasma peptide atlas as a resource for disease proteomics. PMID:18522751
De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. PMID:18493065
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. PMID:18451766
Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. PMID:18408245
PRIDE: new developments and new datasets. PMID:18033805
HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models. PMID:17985986
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. PMID:17984082
Tandem mass spectrometry data quality assessment by self-convolution. PMID:17880728
Advances in proteomic workflows for systems biology. PMID:17698335
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. PMID:17567892
PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories. PMID:17553161
Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. PMID:17437027
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. PMID:17270041
High-accuracy proteome maps of human body fluids. PMID:17140426
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. PMID:17101051
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. PMID:17090601
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. PMID:16901351 -
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
PubMed citations: 212.
212 articles citing: PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas. PMID:35701420
The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community. PMID:35418183
Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways. PMID:35387341
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions. PMID:35225985
The CDK1-TOPBP1-PLK1 axis regulates the Bloom's syndrome helicase BLM to suppress crossover recombination in somatic cells. PMID:35119917
Bioinformatic Analysis and Integration of Transcriptome and Proteome Results Identify Key Coding and Noncoding Genes Predicting Malignancy in Intraductal Papillary Mucinous Neoplasms of the Pancreas. PMID:34790815
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. PMID:34723319
Subcellular proteomics. PMID:34549195
Quantification of Changes in Protein Expression Using SWATH Proteomics. PMID:34236656
Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster. PMID:33575603
The TIM22 complex mediates the import of sideroflexins and is required for efficient mitochondrial one-carbon metabolism. PMID:33476211
Calculating Glycoprotein Similarities From Mass Spectrometric Data. PMID:32883803
Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. PMID:32865986
Evidence That STK19 Is Not an NRAS-dependent Melanoma Driver. PMID:32531245
HIGD2A is Required for Assembly of the COX3 Module of Human Mitochondrial Complex IV. PMID:32317297
Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network. PMID:32053352
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. PMID:31768060
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. PMID:31686107
Proteomics Links Ubiquitin Chain Topology Change to Transcription Factor Activation. PMID:31444107
Genome-wide functional association networks: background, data & state-of-the-art resources. PMID:31281921
A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation. PMID:31142575
Quantitative assay of targeted proteome in tomato trichome glandular cells using a large-scale selected reaction monitoring strategy. PMID:31049073
MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides. PMID:30755466
The PRIDE database and related tools and resources in 2019: improving support for quantification data. PMID:30395289
Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. PMID:30104418
A new SWATH ion library for mouse adult hippocampal neural stem cells. PMID:29896482
A reference peptide database for proteome quantification based on experimental mass spectrum response curves. PMID:29617941
The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. PMID:29386051
Systematic quantitative analysis of H2A and H2B variants by targeted proteomics. PMID:29329550
LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers. PMID:29116567
Functional proteomics outlines the complexity of breast cancer molecular subtypes. PMID:28855612
De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. PMID:28851357
Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer. PMID:28722704
Translational Rodent Models for Research on Parasitic Protozoa-A Review of Confounders and Possibilities. PMID:28638807
Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis. PMID:28486446
Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant. PMID:28261998
Modeling and systematic analysis of biomarker validation using selected reaction monitoring. PMID:28194167
The PeptideAtlas of the Domestic Laying Hen. PMID:28166638
A Golden Age for Working with Public Proteomics Data. PMID:28118949
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. PMID:27924013
Versatile, sensitive liquid chromatography mass spectrometry - Implementation of 10 μm OT columns suitable for small molecules, peptides and proteins. PMID:27897190
Mass Spectrometry-Based Approaches to Understand the Molecular Basis of Memory. PMID:27790611
Determination of differentially regulated proteins upon proteasome inhibition in AML cell lines by the combination of large-scale and targeted quantitative proteomics. PMID:27709814
On the privacy risks of sharing clinical proteomics data. PMID:27595046
Standardized Profiling of The Membrane-Enriched Proteome of Mouse Dorsal Root Ganglia (DRG) Provides Novel Insights Into Chronic Pain. PMID:27103637
De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting. PMID:27056411
Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. PMID:26719571
The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine. PMID:26699206
Systems Proteomics View of the Endogenous Human Claudin Protein Family. PMID:26680015
Common errors in mass spectrometry-based analysis of post-translational modifications. PMID:26667783
Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry. PMID:26633379
Developing Potential Candidates of Preclinical Preeclampsia. PMID:26580600
2016 update of the PRIDE database and its related tools. PMID:26527722
Development of a Targeted Urine Proteome Assay for kidney diseases. PMID:26220717
Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. PMID:26202522
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. PMID:26139527
Targeted proteomics for biomarker discovery and validation of hepatocellular carcinoma in hepatitis C infected patients. PMID:26052377
Introducing the PRIDE Archive RESTful web services. PMID:25904633
Mass spectrometry-based methods for identifying oxidized proteins in disease: advances and challenges. PMID:25874603
Plasma QconCATs reveal a gender-specific proteomic signature in apheresis platelet plasma supernatants. PMID:25743772
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research. PMID:25712262
Impact of allele-specific peptides in proteome quantification. PMID:25676416
Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering. PMID:25660013
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. PMID:25631240
Evidence for lateral gene transfer (LGT) in the evolution of eubacteria-derived small GTPases in plant organelles. PMID:25566271
Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. PMID:25546807
Analysis of alpha-synuclein in malignant melanoma - development of a SRM quantification assay. PMID:25333933
Selected reaction monitoring assays in mesenchymal stem cells from osteoarthritis patients. PMID:25249828
Towards identification of true cancer biomarkers. PMID:25220599
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome. PMID:25152083
Relative quantitation of glycopeptides based on stable isotope labeling using MALDI-TOF MS. PMID:25010467
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. PMID:24939129
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
Protein identification problem from a Bayesian point of view. PMID:24761189
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. PMID:24727770
Conserved peptide fragmentation as a benchmarking tool for mass spectrometers and a discriminating feature for targeted proteomics. PMID:24623587
Mass Spectrometry-based Proteomics and Peptidomics for Systems Biology and Biomarker Discovery. PMID:24504115
The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research. PMID:24436130
Accounting for population variation in targeted proteomics. PMID:24320210
Mass spectrometric protein maps for biomarker discovery and clinical research. PMID:24138574
Cell-cycle regulation of formin-mediated actin cable assembly. PMID:24133141
Grading breast cancer tissues using molecular portraits. PMID:23982162
Plasmodium falciparum malaria: proteomic studies. PMID:23917939
Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. PMID:23842000
A Candida albicans PeptideAtlas. PMID:23811049
Review of software tools for design and analysis of large scale MRM proteomic datasets. PMID:23702368
Oncogenic H-ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition. PMID:23645497
Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. PMID:23579629
From Peptidome to PRIDE: public proteomics data migration at a large scale. PMID:23533138
Targeted quantitation of proteins by mass spectrometry. PMID:23517332
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. PMID:23467006
Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas. PMID:23462206
Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability. PMID:23445834
Controlled vocabularies and ontologies in proteomics: overview, principles and practice. PMID:23429179
Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. PMID:23410677
N-glycoproteome of E14.Tg2a mouse embryonic stem cells. PMID:23405203
A novel spectral library workflow to enhance protein identifications. PMID:23391412
Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. PMID:23388641
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. PMID:23334424
Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. PMID:23250431
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. PMID:23203882
De novo origin of protein-coding genes in murine rodents. PMID:23185269
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
File formats commonly used in mass spectrometry proteomics. PMID:22956731
The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. PMID:22949509
Interfaces to PeptideAtlas: a case study of standard data access systems. PMID:22941959
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. PMID:22865924
Design and application of a data-independent precursor and product ion repository. PMID:22847389
Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles. PMID:22839428
A Bovine PeptideAtlas of milk and mammary gland proteomes. PMID:22837157
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. PMID:22669653
The green proteome: challenges in plant proteomics. PMID:22639573
IQcat: multiplexed protein quantification by isoelectric QconCAT. PMID:22623424
A mass spectrometry proteomics data management platform. PMID:22611296
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. PMID:22588898
Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. PMID:22586326
SRM targeted proteomics in search for biomarkers of HCV-induced progression of fibrosis to cirrhosis in HALT-C patients. PMID:22577025
Using iRT, a normalized retention time for more targeted measurement of peptides. PMID:22577012
Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry. PMID:22543061
PaxDb, a database of protein abundance averages across all three domains of life. PMID:22535208
A computational tool to detect and avoid redundancy in selected reaction monitoring. PMID:22535207
Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach. PMID:22527513
Combining ultracentrifugation and peptide termini group-specific immunoprecipitation for multiplex plasma protein analysis. PMID:22527512
Protein landscape at Drosophila melanogaster telomere-associated sequence repeats. PMID:22493064
PRIDE: quality control in a proteomics data repository. PMID:22434838
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. PMID:22403033
PASSEL: the PeptideAtlas SRMexperiment library. PMID:22318887
PRIDE Inspector: a tool to visualize and validate MS proteomics data. PMID:22318026
Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. PMID:22316387
Analysis of high accuracy, quantitative proteomics data in the MaxQB database. PMID:22301388
TraML--a standard format for exchange of selected reaction monitoring transition lists. PMID:22159873
Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. PMID:22147730
MOPED: Model Organism Protein Expression Database. PMID:22139914
De novo origin of human protein-coding genes. PMID:22102831
Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. PMID:22101334
Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantitation of low abundance protein biomarkers in human plasma. PMID:22098410
Glycoproteomics-based identification of cancer biomarkers. PMID:22084691
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). PMID:22053864
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles). PMID:22052993
Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis. PMID:21997732
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. PMID:21969609
mz5: space- and time-efficient storage of mass spectrometry data sets. PMID:21960719
Verification of male infertility biomarkers in seminal plasma by multiplex selected reaction monitoring assay. PMID:21933954
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets. PMID:21932440
Building and searching tandem mass spectral libraries for peptide identification. PMID:21900153
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. PMID:21876204
CONSeQuence: prediction of reference peptides for absolute quantitative proteomics using consensus machine learning approaches. PMID:21813416
Absolute quantification of microbial proteomes at different states by directed mass spectrometry. PMID:21772258
Spectral archives: a vision for future proteomics data repositories. PMID:21716282
Published and perished? The influence of the searched protein database on the long-term storage of proteomics data. PMID:21700957
Proteomic analysis and discovery using affinity proteomics and mass spectrometry. PMID:21673276
PI: an open-source software package for validation of the SEQUEST result and visualization of mass spectrum. PMID:21672262
Monitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MS. PMID:21637204
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. PMID:21632744
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes. PMID:21571812
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. PMID:21498402
mProphet: automated data processing and statistical validation for large-scale SRM experiments. PMID:21423193
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. PMID:21414234
An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. PMID:21321019
Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. PMID:21293459
Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. PMID:21283140
Coding potential of the products of alternative splicing in human. PMID:21251333
Expression of distinct RNAs from 3' untranslated regions. PMID:21075793
Data management and data integration in the HUPO plasma proteome project. PMID:21063952
Assigning statistical significance to proteotypic peptides via database searches. PMID:21055489
Targeting peptide termini, a novel immunoaffinity approach to reduce complexity in mass spectrometric protein identification. PMID:20962300
Generating and navigating proteome maps using mass spectrometry. PMID:20944666
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. PMID:20816881
Mass spectrometry based glycoproteomics--from a proteomics perspective. PMID:20736408
Widespread protein aggregation as an inherent part of aging in C. elegans. PMID:20711477
Proteomics: a pragmatic perspective. PMID:20622844
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. PMID:20615486
Proteomics of plant pathogenic fungi. PMID:20589070
Elevated level of anterior gradient-2 in pancreatic juice from patients with pre-malignant pancreatic neoplasia. PMID:20550709
Mass-spectrometry-based clinical proteomics--a review and prospective. PMID:20520858
Advancing cardiovascular biology and medicine via proteomics: Opportunities and present challenges of cardiovascular proteomics. PMID:20516387
Synthetic peptide arrays for pathway-level protein monitoring by liquid chromatography-tandem mass spectrometry. PMID:20467045
mspecLINE: bridging knowledge of human disease with the proteome. PMID:20219133
Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays. PMID:20171116
A guided tour of the Trans-Proteomic Pipeline. PMID:20101611
Proteins That Underlie Neoplastic Progression of Ulcerative Colitis. PMID:20098637
Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. PMID:20082347
The PeptideAtlas Project. PMID:20013378
Target-decoy search strategy for mass spectrometry-based proteomics. PMID:20013364
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. PMID:19966807
The Proteomics Identifications database: 2010 update. PMID:19906717
Proteomics data repositories. PMID:19795424
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PMID:19779614
Applying mass spectrometry-based proteomics to genetics, genomics and network biology. PMID:19687803
Serum Proteomic Profiles In Subjects with Heavy Alcohol Abuse. PMID:19672327
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. PMID:19664813
A guide to the Proteomics Identifications Database proteomics data repository. PMID:19662629
Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. PMID:19603825
NCBI Peptidome: a new public repository for mass spectrometry peptide identifications. PMID:19587658
Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. PMID:19411661
Targeted proteomic strategy for clinical biomarker discovery. PMID:19383365
Systems medicine: the future of medical genomics and healthcare. PMID:19348689
Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. PMID:19279071
Founder mutations in the lipase h gene in families with autosomal recessive woolly hair/hypotrichosis. PMID:19262606
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. PMID:19210778
Quantitative interaction proteomics using mass spectrometry. PMID:19198594
Prediction of high-responding peptides for targeted protein assays by mass spectrometry. PMID:19169245
A human proteome detection and quantitation project. PMID:19131327
Systems biology of innate immunity. PMID:19120490
Mass spectrometry based targeted protein quantification: methods and applications. PMID:19105742
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions. PMID:19011259
MAPU 2.0: high-accuracy proteomes mapped to genomes. PMID:18948283 - http://dx.doi.org/10.1093/nar/gkj040
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Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
mass spectrometry spectra
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
proteomics resources
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
dna
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
biology
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
biotechnology
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
blood plasma
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
eukaryotic cells
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
genomes
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
molecular biology
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
peptides
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
proteins
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
proteomics
metasource: re3data.org
version: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:53.805279
small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:53.805279
Tags
More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
mass spectrometry spectra
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PeptideAtlas; PeptideAtlas; DOI: https://doi.org/10.25504/FAIRsharing.dvyrsz; Last edited: Feb. 25, 2021, 10:37 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
proteomics resources
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
dna
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
biology
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
biotechnology
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
blood plasma
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
eukaryotic cells
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
genomes
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
molecular biology
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
peptides
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
proteins
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
proteomics
metasource: re3data.orgversion: re3data.org: PeptideAtlas; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3BK61 last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:53.805279
small molecules
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:53.805279
mass spectrometry spectra molecular structure protein structure proteomics resources dna biotechnology blood plasma eukaryotic cells genomes molecular biology peptides proteins proteomics small molecule
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