| scholarly article | Q13442814 |
| P50 | author | Eric W Deutsch | Q53584947 |
| P2860 | cites work | OpenMS - an open-source software framework for mass spectrometry | Q21284208 |
| UniProt: the Universal Protein knowledgebase | Q24598826 | ||
| Design and implementation of microarray gene expression markup language (MAGE-ML) | Q24803717 | ||
| A statistical model for identifying proteins by tandem mass spectrometry | Q28186251 | ||
| Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search | Q28211385 | ||
| Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France | Q28251402 | ||
| Open mass spectrometry search algorithm | Q28286936 | ||
| mzML: a single, unifying data format for mass spectrometer output | Q28288469 | ||
| A common open representation of mass spectrometry data and its application to proteomics research | Q28291914 | ||
| The mzIdentML data standard for mass spectrometry-based proteomics results | Q28727227 | ||
| mz5: space- and time-efficient storage of mass spectrometry data sets | Q28732283 | ||
| mzML--a community standard for mass spectrometry data | Q28743778 | ||
| The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative | Q28743879 | ||
| MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification | Q29547200 | ||
| TANDEM: matching proteins with tandem mass spectra | Q29615238 | ||
| The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data | Q29618643 | ||
| PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification | Q30053602 | ||
| Skyline: an open source document editor for creating and analyzing targeted proteomics experiments | Q30080030 | ||
| multiplierz: an extensible API based desktop environment for proteomics data analysis. | Q30382070 | ||
| A uniform proteomics MS/MS analysis platform utilizing open XML file formats | Q30478423 | ||
| A guided tour of the Trans-Proteomic Pipeline | Q30497827 | ||
| Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories | Q30996131 | ||
| A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry | Q30996936 | ||
| Should software hold data hostage? | Q33205363 | ||
| Using annotated peptide mass spectrum libraries for protein identification | Q33252895 | ||
| Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries | Q33253787 | ||
| Development and validation of a spectral library searching method for peptide identification from MS/MS. | Q33273391 | ||
| Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics | Q33315747 | ||
| ProteoWizard: open source software for rapid proteomics tools development | Q33349681 | ||
| Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics | Q33393500 | ||
| mzAPI: a new strategy for efficiently sharing mass spectrometry data | Q33424304 | ||
| The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data | Q33428180 | ||
| Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. | Q33775524 | ||
| compomics-utilities: an open-source Java library for computational proteomics | Q33840310 | ||
| ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry | Q33849501 | ||
| mProphet: automated data processing and statistical validation for large-scale SRM experiments | Q33851184 | ||
| jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions | Q34038598 | ||
| ProHits: integrated software for mass spectrometry-based interaction proteomics | Q34211917 | ||
| jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats | Q34249159 | ||
| Automated selected reaction monitoring software for accurate label-free protein quantification | Q34289600 | ||
| PRIDE: the proteomics identifications database | Q34436630 | ||
| The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards | Q35497527 | ||
| PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows | Q36638849 | ||
| The PSI formal document process and its implementation on the PSI website | Q36849890 | ||
| PEPPeR, a platform for experimental proteomic pattern recognition. | Q37113905 | ||
| Comprehensive proteomics | Q37796132 | ||
| MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. | Q38461368 | ||
| TraML--a standard format for exchange of selected reaction monitoring transition lists | Q38479687 | ||
| PRIDE Converter: making proteomics data-sharing easy | Q42627061 | ||
| SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling | Q42630073 | ||
| PROTEIOS: an open source proteomics initiative | Q42647064 | ||
| Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands | Q44199955 | ||
| Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea | Q45197966 | ||
| InsPecT: identification of posttranslationally modified peptides from tandem mass spectra | Q46259455 | ||
| A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS. | Q48444121 | ||
| Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low-femtomole level. | Q53856036 | ||
| The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics | Q56889083 | ||
| P433 | issue | 12 | |
| P921 | main subject | file format | Q235557 |
| P304 | page(s) | 1612-1621 | |
| P577 | publication date | 2012-09-06 | |
| P1433 | published in | Molecular & Cellular Proteomics | Q6895932 |
| P1476 | title | File formats commonly used in mass spectrometry proteomics | |
| P478 | volume | 11 |
| Q47964163 | A Computational Tool for Accelerated Analysis of Oligomeric Proanthocyanidins in Plants |
| Q37432423 | A multicenter study benchmarks software tools for label-free proteome quantification |
| Q62020441 | Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics |
| Q41982219 | Analytical utility of mass spectral binning in proteomic experiments by SPectral Immonium Ion Detection (SPIID). |
| Q47680249 | Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows |
| Q34691984 | Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities |
| Q30891496 | Building high-quality assay libraries for targeted analysis of SWATH MS data |
| Q33784953 | Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum. |
| Q37160902 | Combining results of multiple search engines in proteomics |
| Q58731469 | Comprehensive high-resolution multiple-reaction monitoring mass spectrometry for targeted eicosanoid assays |
| Q27005933 | Computational phosphoproteomics: from identification to localization |
| Q34594396 | Controlled vocabularies and ontologies in proteomics: overview, principles and practice |
| Q105826365 | Global chemical analysis of biology by mass spectrometry |
| Q34606966 | Haystack, a web-based tool for metabolomics research |
| Q30738680 | MASSyPup--an 'out of the box' solution for the analysis of mass spectrometry data |
| Q33583211 | MS-viewer: a web-based spectral viewer for proteomics results |
| Q30596948 | Management and dissemination of MS proteomic data with PROTICdb: example of a quantitative comparison between methods of protein extraction |
| Q38904134 | MathIOmica-MSViewer: a dynamic viewer for mass spectrometry files for Mathematica. |
| Q28068009 | Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations |
| Q28660368 | Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective |
| Q28278187 | OpenMS: a flexible open-source software platform for mass spectrometry data analysis |
| Q48317444 | OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data |
| Q27311603 | PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets |
| Q91651576 | PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms |
| Q31148953 | Platforms and Pipelines for Proteomics Data Analysis and Management |
| Q47318874 | Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night |
| Q64109164 | Proteomics Standards Initiative Extended FASTA Format |
| Q92377449 | SPECTRUM - A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data |
| Q53833187 | Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics. |
| Q38371542 | The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. |
| Q36164068 | The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5. |
| Q28646890 | Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics |
| Q31164882 | compMS2Miner: An Automatable Metabolite Identification, Visualization, and Data-Sharing R Package for High-Resolution LC-MS Data Sets. |
| Q34506492 | iPiG: integrating peptide spectrum matches into genome browser visualizations |
| Q38430038 | multiplierz v2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data |
| Q30878078 | mzDB: a file format using multiple indexing strategies for the efficient analysis of large LC-MS/MS and SWATH-MS data sets |
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