0000000000262225

AUTHOR

Miguel Marcilla

0000-0001-9171-5076

showing 6 related works from this author

An open-source computational and data resource to analyze digital maps of immunopeptidomes

2015

We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the de…

Databases FactualimmunopeptidomeQH301-705.5Systems biologyScienceImmunologyComputational biologyBiologyBioinformaticsMass spectrometryGeneral Biochemistry Genetics and Molecular BiologyMass Spectrometry03 medical and health sciencesResource (project management)Fragment (logic)HLA Antigenstargeted mass spectrometryHigh-Throughput Screening AssaysDIAhumanAntigenshuman leukocytes antigenBiology (General)030304 developmental biology0303 health sciencesAntigen PresentationGeneral Immunology and MicrobiologyDigital mappingGeneral Neuroscience030302 biochemistry & molecular biologyQRComputational BiologyGeneral Medicine3. Good healthTools and ResourcesHigh-Throughput Screening AssaysWorkflowTargeted mass spectrometrySWATH-MSMedicinePeptidesComputational and Systems BiologyeLife
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Multicentric study of the effect of pre-analytical variables in the quality of plasma samples stored in biobanks using different complementary proteo…

2016

12 páginas, 7 figuras.-- Jesús Mateos ... et al.

0301 basic medicineProteomicsAdultMaleQuality ControlSample (material)Sample processingBiophysicsProteomicsBioinformaticsBiochemistrySpecimen HandlingSample03 medical and health sciencesPlasmaYoung AdultProtein stabilityHumansBiobankAgedBiological Specimen BanksAged 80 and overBlood Specimen CollectionChromatographyPlasma samplesChemistryPre analyticalProtein StabilityPre-analytical variablesMiddle AgedBlood proteinsBiobanks030104 developmental biologyBlood PreservationResearch studiesFemale
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Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE)

2018

Minimal Information about an Immuno-Peptidomics Experiment (MIAIPE) is an initiative of the members of the Human Immuno-Peptidome Project (HIPP), an international program organized by the Human Proteome Organization (HUPO). The aim of the MIAIPE guidelines is to deliver technical guidelines representing the minimal information required to sufficiently support the evaluation and interpretation of immunopeptidomics experiments. The MIAIPE document has been designed to report essential information about sample preparation, mass spectrometric measurement and associated mass spectrometry (MS)-related bioinformatics aspects that are unique to immunopeptidomics and may not be covered by the genera…

Proteomics0301 basic medicineComputer scienceComputational biologyProteomicsBiochemistrySpecimen Handling03 medical and health sciencesStandardisation & GuidelinesHuman proteome projectHumansantigen processing and presentationDatabases ProteinMolecular Biology030102 biochemistry & molecular biologyHistocompatibility Antigens Class IHistocompatibility Antigens Class IIimmunopeptidomicsComputational BiologyMass spectrometricPeptide Fragmentsmajor histocompatibility complex3. Good health030104 developmental biologyComputational Biology/standards; Databases Protein; Histocompatibility Antigens Class I/analysis; Histocompatibility Antigens Class I/immunology; Histocompatibility Antigens Class I/metabolism; Histocompatibility Antigens Class II/analysis; Histocompatibility Antigens Class II/immunology; Histocompatibility Antigens Class II/metabolism; Humans; Peptide Fragments/analysis; Peptide Fragments/immunology; Peptide Fragments/metabolism; Proteomics/standards; Software; Specimen Handling/standards; antigen processing and presentation; immunopeptidomics; major histocompatibility complexSoftwareantigen processing and presentation; immunopeptidomics; major histocompatibility complex
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Author response: An open-source computational and data resource to analyze digital maps of immunopeptidomes

2015

Open sourceResource (project management)DatabaseDigital mappingComputer sciencecomputer.software_genrecomputer
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A multicentric study to evaluate the use of relative retention times in targeted proteomics.

2016

Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results…

0301 basic medicineMultiple reaction monitoringProteomicsBiomedical ResearchComputer scienceBiophysicsLiquid chromatographyContext (language use)BioinformaticsBiochemistry03 medical and health sciencesInter-laboratory validationTargeted proteomicsObserver VariationReproducibilityResearchReproducibility of ResultsAnalytical scienceReference StandardsStandardizationReproducibilityCell and molecular biologyTargeted proteomics030104 developmental biologyBiological significanceBiochemical engineeringRetention timeChromatography LiquidJournal of proteomics
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Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome

2013

All participating laboratories are members of ProteoRed-ISCIII.-- et al.

ProteomicsProteomeSequence analysisBioinformaticsBiologyMicrobiologíaENCODEProteomicsBiochemistryMass SpectrometryTranscriptome03 medical and health sciencesAnnotationChromosome 16RNA-Seq. ENCODEHuman proteome projectHumansHuman proteome projectTranscriptomics030304 developmental biologyGenetics0303 health sciencesSequence Analysis RNA030302 biochemistry & molecular biologyGeneral ChemistryChromosome 163. Good healthProteomeTranscriptomeChromosomes Human Pair 16Chromatography Liquid
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