The Global Proteome Machine Database
Names
More detailed information about this field from each metasource.
The Global Proteome Machine Database
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gpmDB
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Names
More detailed information about this field from each metasource.
The Global Proteome Machine Database
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gpmDB
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Names
More detailed information about this field from each metasource.
The Global Proteome Machine Database
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
gpmDB
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.
Description
More detailed information about this field from each metasource.
The Global Proteome Machine Database (gpmDB holds the minimum amount of information necessary for common bioinformatics-related tasks (such as sequence assignment validation) rather than being a complete record of a proteomics experiment. It was also created to aid in the process of validating peptide MS/MS spectra as well as protein coverage patterns. Most of the data is held in a set of XML files: the database serves as an index to those files, allowing for rapid lookups and reduced database storage requirements.
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Webpage:
https://www.thegpm.org/GPMDB/index.htmlWebpage
More detailed information about this field from each metasource.
https://www.thegpm.org/GPMDB/index.html
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Open source system for analyzing, validating, and storing protein identification data
PMID: 15595733
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
Open source system for analyzing, validating, and storing protein identification data
PMID: 15595733
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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Open source system for analyzing, validating, and storing protein identification data
PubMed citations: 255.
255 articles citing: Open source system for analyzing, validating, and storing protein identification data
Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line. PMID:35601313
Exploring synergies between plant metabolic modelling and machine learning. PMID:35521559
The PeptideAtlas of a widely cultivated fish Labeo rohita: A resource for the Aquaculture Community. PMID:35418183
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
LRP1 loss in airway epithelium exacerbates smoke-induced oxidative damage and airway remodeling. PMID:35202607
Prediction of Peptide Detectability Based on CapsNet and Convolutional Block Attention Module. PMID:34769509
Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses. PMID:34740240
Deep representation features from DreamDIAXMBD improve the analysis of data-independent acquisition proteomics. PMID:34650228
CircNCX1: the "Lord of the Ring" in the Heart - Insight into Its Sequence Characteristic, Expression, Molecular Mechanisms, and Clinical Application. PMID:34642871
A proteomics sample metadata representation for multiomics integration and big data analysis. PMID:34615866
Sample Preparation Strategies for Antibody-Free Quantitative Analysis of High Mobility Group Box 1 Protein. PMID:34205112
RGS14 Regulation of Post-Synaptic Signaling and Spine Plasticity in Brain. PMID:34201943
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
A spatiotemporal molecular switch governs plant asymmetric cell division. PMID:33941907
Bacterial Hsp90 Facilitates the Degradation of Aggregation-Prone Hsp70-Hsp40 Substrates. PMID:33937334
Proteomic Profiling and Artificial Intelligence for Hepatocellular Carcinoma Translational Medicine. PMID:33562077
Alcohol Increases Exosome Release from Microglia to Promote Complement C1q-Induced Cellular Death of Proopiomelanocortin Neurons in the Hypothalamus in a Rat Model of Fetal Alcohol Spectrum Disorders. PMID:32887744
Schistosoma haematobium Extracellular Vesicle Proteins Confer Protection in a Heterologous Model of Schistosomiasis. PMID:32722279
Characterization of glutathione proteome in CHO cells and its relationship with productivity and cholesterol synthesis. PMID:32662871
Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code. PMID:32518165
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
Glycomics and glycoproteomics of viruses: Mass spectrometry applications and insights toward structure-function relationships. PMID:32350911
Regulation of reactive oxygen species during plant immunity through phosphorylation and ubiquitination of RBOHD. PMID:32296066
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. PMID:31686107
Delineating the contribution of Spc105-bound PP1 to spindle checkpoint silencing and kinetochore microtubule attachment regulation. PMID:31649151
N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. PMID:31516400
Analysis of Brain and Cerebrospinal Fluid from Mouse Models of the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Changes in the Lysosomal Proteome. PMID:31501224
MassComp, a lossless compressor for mass spectrometry data. PMID:31262247
Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results. PMID:31260318
Identification of a Multiplex Biomarker Panel for Hypertrophic Cardiomyopathy Using Quantitative Proteomics and Machine Learning. PMID:31243064
Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. PMID:31076411
Development of screening strategies for the identification of paramylon-degrading enzymes. PMID:30806871
Computational and experimental analysis of bioactive peptide linear motifs in the integrin adhesome. PMID:30689642
Mesencephalic astrocyte-derived neurotropic factor is an important factor in chondrocyte ER homeostasis. PMID:30543055
Clinical potential of mass spectrometry-based proteogenomics. PMID:30487530
Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma. PMID:30402543
The PRIDE database and related tools and resources in 2019: improving support for quantification data. PMID:30395289
Expanding the Use of Spectral Libraries in Proteomics. PMID:30270626
Approaches to the discovery of non-invasive urinary biomarkers of prostate cancer. PMID:30197761
Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. PMID:30104418
A tissue-based draft map of the murine MHC class I immunopeptidome. PMID:30084848
Proteomic Changes in Mouse Spleen after Radiation-Induced Injury and its Modulation by Gamma-Tocotrienol. PMID:30070965
Quantification of Inflammasome Adaptor Protein ASC in Biological Samples by Multiple-Reaction Monitoring Mass Spectrometry. PMID:29948504
PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ. PMID:29934401
Public proteomics data: How the field has evolved from sceptical inquiry to the promise of in silico proteomics. PMID:29900110
Understanding Leishmania parasites through proteomics and implications for the clinic. PMID:29717934
AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation. PMID:29599191
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction. PMID:29409446
Protein biomarkers for subtyping breast cancer and implications for future research. PMID:29271260
MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting. PMID:29192002
Proteomic analysis of lung metastases in a murine breast cancer model reveals divergent influence of CTSB and CTSL overexpression. PMID:29187882
LC-SRM-Based Targeted Quantification of Urinary Protein Biomarkers. PMID:29116567
ProteomicsDB. PMID:29106664
Preservation of the metaproteome: variability of protein preservation in ancient dental calculus. PMID:29098079
Enhanced Missing Proteins Detection in NCI60 Cell Lines Using an Integrative Search Engine Approach. PMID:28960077
Dynamic N-glycoproteome analysis of maize seedling leaves during de-etiolation using Concanavalin A lectin affinity chromatography and a nano-LC-MS/MS-based iTRAQ approach. PMID:28942497
CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo. PMID:28819186
Proteomic Analysis of Brain and Cerebrospinal Fluid from the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Potential Biomarkers. PMID:28792770
Food allergen detection by mass spectrometry: the role of systems biology. PMID:28725476
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. PMID:28721231
The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics. PMID:28691345
Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs. PMID:28480704
Multilevel regulation of an α-arrestin by glucose depletion controls hexose transporter endocytosis. PMID:28468835
Methods, Tools and Current Perspectives in Proteogenomics. PMID:28456751
A Basic ApoE-Based Peptide Mediator to Deliver Proteins across the Blood-Brain Barrier: Long-Term Efficacy, Toxicity, and Mechanism. PMID:28456380
Identifying the missing proteins in human proteome by biological language model. PMID:28155671
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
Tapered-Tip Capillary Electrophoresis Nano-Electrospray Ionization Mass Spectrometry for Ultrasensitive Proteomics: the Mouse Cortex. PMID:27853976
Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli. PMID:27713404
53BP1 ablation rescues genomic instability in mice expressing 'RING-less' BRCA1. PMID:27670884
Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence. PMID:27581094
Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. PMID:27577934
A Skyline Plugin for Pathway-Centric Data Browsing. PMID:27530777
Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. PMID:27493588
Advances in targeted proteomics and applications to biomedical research. PMID:27302376
ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles. PMID:27068479
De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting. PMID:27056411
Urine Proteome Biomarkers in Kidney Diseases. I. Limits, Perspectives, and First Focus on Normal Urine. PMID:26997865
A first dataset toward a standardized community-driven global mapping of the human immunopeptidome. PMID:26958639
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
Proteogenomics from a bioinformatics angle: A growing field. PMID:26670565
Ion Activation Methods for Peptides and Proteins. PMID:26630359
Identification of novel CSF biomarkers for neurodegeneration and their validation by a high-throughput multiplexed targeted proteomic assay. PMID:26627638
Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics. PMID:26569054
2016 update of the PRIDE database and its related tools. PMID:26527722
Exploring the potential of public proteomics data. PMID:26449181
Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification. PMID:26325288
CDK8-Cyclin C Mediates Nutritional Regulation of Developmental Transitions through the Ecdysone Receptor in Drosophila. PMID:26222308
Autophagy is induced upon platelet activation and is essential for hemostasis and thrombosis. PMID:26209658
MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. PMID:26204236
Targeted Proteomics-Driven Computational Modeling of Macrophage S1P Chemosensing. PMID:26199343
Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. PMID:26193931
An open-source computational and data resource to analyze digital maps of immunopeptidomes. PMID:26154972
Improving protein identification from tandem mass spectrometry data by one-step methods and integrating data from other platforms. PMID:26141827
State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. PMID:26139527
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. PMID:26061177
Multidimensional proteomics for cell biology. PMID:25857810
Plasma QconCATs reveal a gender-specific proteomic signature in apheresis platelet plasma supernatants. PMID:25743772
Web resources for mass spectrometry-based proteomics. PMID:25721607
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
Binding of Kif23-iso1/CHO1 to 14-3-3 is regulated by sequential phosphorylations at two LATS kinase consensus sites. PMID:25658096
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. PMID:25656970
Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. PMID:25631240
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. PMID:25599550
A public repository for mass spectrometry imaging data. PMID:25542566
Altered Transcriptional Control Networks with Trans-Differentiation of Isogenic Mutant-KRas NSCLC Models. PMID:25538889
Current peptidomics: applications, purification, identification, quantification, and functional analysis. PMID:25429922
Identifying novel biomarkers through data mining-a realistic scenario? PMID:25347964
Analysis of the tryptic search space in UniProt databases. PMID:25307260
Mass spec studio for integrative structural biology. PMID:25242457
PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species. PMID:25228907
Identification of long-lived proteins retained in cells undergoing repeated asymmetric divisions. PMID:25228775
Towards identification of true cancer biomarkers. PMID:25220599
Crux: rapid open source protein tandem mass spectrometry analysis. PMID:25182276
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
Expediting SRM assay development for large-scale targeted proteomics experiments. PMID:25145539
Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS. PMID:25026199
CPTAC Assay Portal: a repository of targeted proteomic assays. PMID:24972168
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. PMID:24939910
Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. PMID:24939129
The C-score: a Bayesian framework to sharply improve proteoform scoring in high-throughput top down proteomics. PMID:24922115
A draft map of the human proteome. PMID:24870542
PIQMIe: a web server for semi-quantitative proteomics data management and analysis. PMID:24861615
Low abundance of the matrix arm of complex I in mitochondria predicts longevity in mice. PMID:24815183
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
ProteomeXchange provides globally coordinated proteomics data submission and dissemination. PMID:24727771
Adenovirus composition, proteolysis, and disassembly studied by in-depth qualitative and quantitative proteomics. PMID:24591515
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
MOPED enables discoveries through consistently processed proteomics data. PMID:24350770
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
Mass spectrometric protein maps for biomarker discovery and clinical research. PMID:24138574
Assessment of marker proteins identified in whole cell extracts for bacterial speciation using liquid chromatography electrospray ionization tandem mass spectrometry. PMID:23994725
Proteomic and systems biology analysis of the monocyte response to Coxiella burnetii infection. PMID:23990884
A fast Peptide Match service for UniProt Knowledgebase. PMID:23958731
A Candida albicans PeptideAtlas. PMID:23811049
Acclimation to different depths by the marine angiosperm Posidonia oceanica: transcriptomic and proteomic profiles. PMID:23785376
Review of software tools for design and analysis of large scale MRM proteomic datasets. PMID:23702368
Serine protease HtrA1 accumulates in corneal transforming growth factor beta induced protein (TGFBIp) amyloid deposits. PMID:23592924
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
Extending the mannose 6-phosphate glycoproteome by high resolution/accuracy mass spectrometry analysis of control and acid phosphatase 5-deficient mice. PMID:23478313
Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. PMID:23467006
Quantitation of the dynamic profiles of the innate immune response using multiplex selected reaction monitoring-mass spectrometry. PMID:23418394
Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. PMID:23410677
Context-sensitive markov models for peptide scoring and identification from tandem mass spectrometry. PMID:23289783
Systems biology, bioinformatics, and biomarkers in neuropsychiatry. PMID:23269912
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
The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. PMID:23203882
Unleashing the power of proteomics to develop blood-based cancer markers. PMID:23099557
Proteomic analysis of mouse models of Niemann-Pick C disease reveals alterations in the steady-state levels of lysosomal proteins within the brain. PMID:23070805
The Units Ontology: a tool for integrating units of measurement in science. PMID:23060432
Proteomic and systems biology analysis of monocytes exposed to securinine, a GABA(A) receptor antagonist and immune adjuvant. PMID:23028424
Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression. PMID:22994686
GENCODE: the reference human genome annotation for The ENCODE Project. PMID:22955987
Mass spectrometry for translational proteomics: progress and clinical implications. PMID:22943415
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
Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. PMID:22669653
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. PMID:22588898
The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. PMID:22577014
PaxDb, a database of protein abundance averages across all three domains of life. PMID:22535208
Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. PMID:22446687
PRIDE: quality control in a proteomics data repository. PMID:22434838
The mzIdentML data standard for mass spectrometry-based proteomics results. PMID:22375074
PASSEL: the PeptideAtlas SRMexperiment library. PMID:22318887
Analysis of high accuracy, quantitative proteomics data in the MaxQB database. PMID:22301388
Cut-like homeobox 1 and nuclear factor I/B mediate ENGRAILED2 autism spectrum disorder-associated haplotype function. PMID:22180456
TraML--a standard format for exchange of selected reaction monitoring transition lists. PMID:22159873
MOPED: Model Organism Protein Expression Database. PMID:22139914
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
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
18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry. PMID:21988777
miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. PMID:21984185
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
Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. PMID:21931151
Biobank resources for future patient care: developments, principles and concepts. PMID:21923917
Building and searching tandem mass spectral libraries for peptide identification. PMID:21900153
Comparison of Programmatic Approaches for Efficient Accessing to mzML Files. PMID:21766049
The human proteome project: current state and future direction. PMID:21742803
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes. PMID:21571812
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
Index-ion triggered MS2 ion quantification: a novel proteomics approach for reproducible detection and quantification of targeted proteins in complex mixtures. PMID:21169564
An empirical strategy for characterizing bacterial proteomes across species in the absence of genomic sequences. PMID:21103051
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
Identification of chemical-adducted proteins in urine by multi-dimensional protein identification technology (LC/LC-MS/MS). PMID:20972764
Utilization of LC-MS/MS analyses to identify site-specific chemical protein adducts in vitro. PMID:20972762
The program for processing newly synthesized histones H3.1 and H4. PMID:20953179
Generating and navigating proteome maps using mass spectrometry. PMID:20944666
Mass spectrometric protein identification using the global proteome machine. PMID:20835799
The grand challenge to decipher the cancer proteome. PMID:20733593
A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra. PMID:20731867
mzML--a community standard for mass spectrometry data. PMID:20716697
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. PMID:20677327
Increased selectivity, analytical precision, and throughput in targeted proteomics. PMID:20664071
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
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
ProteomeCommons.org collaborative annotation and project management resource integrated with the Tranche repository. PMID:20356086
Arginine methylation controls the subcellular localization and functions of the oncoprotein splicing factor SF2/ASF. PMID:20308322
The PeptideAtlas Project. PMID:20013378
Detection of differentially expressed basal cell proteins by mass spectrometry. PMID:19955077
NCBI Peptidome: a new repository for mass spectrometry proteomics data. PMID:19942688
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. PMID:19941647
The Proteomics Identifications database: 2010 update. PMID:19906717
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PMID:19779614
A guide to the Proteomics Identifications Database proteomics data repository. PMID:19662629
Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. PMID:19608599
Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. PMID:19411661
Mass spectrometry-based protein profiling to determine the cause of lysosomal storage diseases of unknown etiology. PMID:19383612
MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides. PMID:19327145
Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. PMID:19326923
A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra. PMID:19288523
MassMatrix: a database search program for rapid characterization of proteins and peptides from tandem mass spectrometry data. PMID:19235167
Prediction of high-responding peptides for targeted protein assays by mass spectrometry. PMID:19169245
A human proteome detection and quantitation project. PMID:19131327
Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring. PMID:19121650
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. PMID:19087293
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
Selected reaction monitoring for quantitative proteomics: a tutorial. PMID:18854821
A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time. PMID:18713471
Challenges and solutions in proteomics. PMID:18645629
Phosphoprotein profiling by PA-GeLC-MS/MS. PMID:18510356
The mannose 6-phosphate glycoprotein proteome. PMID:18507433
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. PMID:18451766
ISPIDER Central: an integrated database web-server for proteomics. PMID:18440977
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification. PMID:18187442
Advances in proteomic workflows for systems biology. PMID:17698335
Introduction to computational proteomics. PMID:17676979
Mutations in the Type II protein arginine methyltransferase AtPRMT5 result in pleiotropic developmental defects in Arabidopsis. PMID:17573539
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
Pulmonary biomarkers based on alterations in protein expression after exposure to arsenic. PMID:17450228
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
Hair bundles are specialized for ATP delivery via creatine kinase. PMID:17270734
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. PMID:17270041
Proteomic analysis of cervical-vaginal fluid: identification of novel biomarkers for detection of intra-amniotic infection. PMID:17203952
Verification of single-peptide protein identifications by the application of complementary database search algorithms. PMID:17122065
The chloride intracellular channel protein CLIC5 is expressed at high levels in hair cell stereocilia and is essential for normal inner ear function. PMID:17021174
The wildcat toolbox: a set of perl script utilities for use in peptide mass spectral database searching and proteomics experiments. PMID:16741236
Identification of methylation sites in Thermotoga maritima chemotaxis receptors. PMID:16707700
PRIDE: a public repository of protein and peptide identifications for the proteomics community. PMID:16381953
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. PMID:16381951
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mass spectrometry assay
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
mass spectrometry spectra
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
proteome
metasource: Fairsharing.org
version: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Tags
More detailed information about this field from each metasource.
mass spectrometry assay
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
mass spectrometry spectra
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
proteome
metasource: Fairsharing.orgversion: FAIRsharing.org: gpmDB; The Global Proteome Machine Database; DOI: https://doi.org/10.25504/FAIRsharing.fhcmwq; Last edited: Feb. 25, 2021, 12:09 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
mass spectrometry assay mass spectrometry spectra molecular interaction protein proteome
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