Herbert M S MS - OmicsDI

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Unknown (134)
Proteomics (39)
Transcriptomics (13)
Metabolomics (7)
Genomics (1)

Organisms

Homo sapiens (28)
Mus musculus (14)
Saccharomyces cerevisiae (2)
Rattus norvegicus (2)
Ambystoma mexicanum (1)
Staphylococcus aureus subsp. aureus USA300 (1)
Streptomyces coelicolor A3(2) (1)
Halobacterium salinarum NRC-1 (1)
Bos taurus (1)
Escherichia coli (1)
Schizosaccharomyces pombe 927 (1)
Staphylococcus aureus subsp. aureus NCTC 8325 (1)
Sus scrofa domesticus (1)
Trichomonas vaginalis (1)
Trichomonas vaginalis G3 (1)

Repository

pride (37)
biostudies-arrayexpress (13)
MetaboLights (7)
EGA (1)
MassIVE (1)
PeptideAtlas (1)

Tissue

Cell culture (8)
Retina (6)
Lung (5)
Blood serum (3)
Retinal cell (3)
Blood cell (2)
Blood plasma (2)
Cell suspension culture (2)
Epithelial cell (2)
Adipocyte (1)
Blood (1)
Brain (1)
Cardiovascular system (1)
Diaphragm (1)
Fibroblast (1)
HT-1080 cell (1)
Kidney (1)
Monocyte (1)
Permanent cell line cell (1)
Photoreceptor cell (1)
Retinal pigment epithelial cell (1)

Disease

Retinal degeneration (4)
Trichomoniasis (2)
Acute leukemia (1)
Brain glioblastoma multiforme (1)
COVID-19 (1)
Cell type cancer (1)
Dementia (1)
Disease free (1)
Idiopathic pulmonary fibrosis (1)
Plasmodium falciparum malaria (1)

Technology Type

Mass Spectrometry (37)
Shotgun proteomics (15)
Bottom-up proteomics (10)
Data-dependent acquisition (7)
Mass spectrometry (6)
Affinity purification coupled with mass spectrometry proteomics (3)
SRM/MRM (2)
NMR spectroscopy (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
Data-independent acquisition (1)
Gel-based experiment (1)
Glycoproteomics (1)
HDMSE (1)
Top-down proteomics (1)

Instrument Platform

Illumina NovaSeq 6000 (1)
Orbitrap Exploris 480 (1)
Autoflex speed smartbeam (1)
Bruker (1)
Exactive (1)
LTQ Orbitrap XL ETD (1)
LTQ Velos (Thermo Scientific) (1)
Liquid Chromatography MS - alternating - reverse phase (1)
Liquid Chromatography MS - negative - reverse phase (1)
Unknown (1)

Publication Date

2024 (10)
2026 (7)
2025 (6)
2019 (5)
2021 (5)
2020 (4)
2022 (3)
2016 (3)
2015 (3)
2013 (2)
2011 (2)
2010 (2)
2023 (2)
2014 (1)
2008 (1)
2007 (1)
2017 (1)
2006 (1)

CHEBI ID

CHEBI:64591 (2)
CHEBI:64592 (2)
CHEBI:64593 (2)
CHEBI:131427 (1)
CHEBI:131428 (1)
CHEBI:131430 (1)
CHEBI:131991 (1)
CHEBI:132004 (1)
CHEBI:132007 (1)
CHEBI:132033 (1)
CHEBI:134239 (1)
CHEBI:134241 (1)
CHEBI:134242 (1)
CHEBI:134270 (1)
CHEBI:134271 (1)
CHEBI:134428 (1)
CHEBI:134435 (1)
CHEBI:134439 (1)
CHEBI:134494 (1)
CHEBI:134648 (1)
CHEBI:136234 (1)
CHEBI:136235 (1)
CHEBI:136236 (1)
CHEBI:136239 (1)
CHEBI:136245 (1)
CHEBI:136247 (1)
CHEBI:136252 (1)
CHEBI:136256 (1)
CHEBI:136257 (1)
CHEBI:136258 (1)

Metabolite Name

(+)-Syringaresinol O-beta-D-glucoside (1)
(+)-secoisolariciresinol diglucoside (1)
(-)-11-hydroxy-9,10-dihydrojasmonic acid 11-beta-D-glucoside (1)
(-)-Columbianetin (1)
(-)-Epigallocatechin 3-gallate 7-glucoside 4"-glucuronide (1)
(-)-Jasmonic acid (1)
(-)-epicatechin (1)
(15S)-15-Hydroxy-5,8,11-cis-13-trans-eicosatetraenoate (1)
(2S)-2-Butanol O-[b-D-Apiofuranosyl-(1->6)-b-D-glucopyranoside] (1)
(2S)-2-hydroxybutanedioic acid (1)
(2b,3b)-Dihydroxy-30-nor-12,20(29)-oleanadiene-28-glucopyranosyloxy-23-oic acid 3-glucuronide (1)
(6Z,9Z,12Z)-Octadecatrienoic acid (1)
(7'R)-(+)-Lyoniresinol 9'-glucoside (1)
(9R,10R)-Dihydroxyoctadecanoic acid (1)
(9Z)-(7S,8S)-Dihydroxyoctadecenoic acid (1)
(9Z)-Hexadecenoic acid (1)
(9Z)-Octadecenoic acid (1)
(9Z,12Z)-(8R)-Hydroxyoctadeca-9,12-dienoic acid (1)
(R)-(Homo)3-citrate (1)
(R)-1-O-[b-D-Glucopyranosyl-(1->6)-b-D-glucopyranoside]-1,3-octanediol (1)
(R)-5-Phosphomevalonate (1)
(S)-Malate (1)
(S)-Multifidol 2-[apiosyl-(1->6)-glucoside] (1)
(Z)-Resveratrol 3,4-diglucoside (1)
1,5-Dihydroxy-4,8-bis(hydroxy(hydroxymethyl)amino)anthraquinone (1)
1,8-Diazacyclotetradecane-2,9-dione (1)
1-Caffeoyl-4-deoxyquinic acid (1)
1-O-Galloyl-beta-D-glucose (1)
1-O-Sinapoyl-beta-D-glucose (1)
1-Octen-3-ol-3-o-beta-D-xylopyranosyl(1->6)-beta-D-glucopyranoside (1)

Study type

Transcription profiling by array (7)
RNA-seq of coding RNA (2)
Transcription profiling by SAGE (1)
Unknown experiment type (1)
Genotyping by array (1)
Spatial transcriptomics by high-throughput sequencing (1)

Release Date

2022 (24)
2025 (18)
2023 (18)
2021 (16)
2024 (12)
2014 (9)
2020 (8)
2015 (7)
2019 (6)
2008 (6)
2016 (4)
2013 (4)
2011 (3)
2010 (3)
2018 (3)
2017 (2)
2012 (2)
2007 (1)
2026 (1)

Lab affiliation

Center for Translational Vision Research, Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, 92697, USA; Department of Physiology and Biophysics, Department of Chemistry, Department of Molecular Biology and Biochemistry; University of California, Irvine, Irvine, CA, 92697, USA (3)
Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic (2)
Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany (2)
Institute of Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, German (2)
1. Gavin Herbert Eye Institute - Center for Translational Vision Research, Department of Ophthalmology, University of California Irvine, CA, 92697, USA 2. Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA (1)
1.Center for Translational Vision Research, Gavin Herbert Eye Institute, Department of Ophthalmology, University of California-Irvine, Irvine, CA 92697, USA 2.Department of Ophthalmic Research, Cleveland Clinic, Cleveland, OH 44195, USA 3.Department of Physiology & Biophysics, School of Medicine, University of California-Irvine, Irvine, CA 92697, USA (1)
1Brunason Center for Translational Vision Research, Department of Ophthalmology and Visual Sciences, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, 92697, USA; 2Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA; 3Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697, USA (1)
Assistant Professor Department of Cellular and Molecular Medicine Florida International University | Herbert Wertheim College of Medicine (1)
Assistant Professor & K12 Scholar Translational Glycobiology Institute, Department of Translational Medicine Florida International University | Herbert Wertheim College of Medicine (1)
Assistant Professor Department of Cellular and Molecular Medicine Florida International University | Herbert Wertheim College of Medicine (1)
Assistant Professor Department of Medicine | Cardiology | Cardiometabolic Precision Medicine Program Department of Systems Biology Herbert Irving Comprehensive Cancer Center | Precision Oncology and Systems Biology Program Data Science Institute | Health Analytics Center Columbia Stem Cell Initiative Columbia University Irving Medical Center 630 West 168th Street, P&S 10-401, New York, NY 10032 (1)
Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, School of Molecular and Cellular Bilogy, University of Leeds, LS2 9JT (1)
Cell Signaling and Chemical Biology, Research Unit Signaling and Translation, Helmholtz Zentrum München, Neuherberg, Germany; Department of Biological Sciences, Department of Chemistry, Herbert Irving Comprehensive Cancer Center, Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA. (1)
Center for Infectious Diseases Research Department of Pathology and Genomic Medicine Houston Methodist Research Institute USA (1)
Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; CECAD, University of Cologne, Faculty of Medicine and University Hospital Cologne, Germany (1)
Department of Genetics and Development Herbert Irving Comprehensive Cancer Center Columbia University Irving Medical Center New York, NY, USA (1)
Department of Pathology and Cell Biology and Institute for Cancer Genetics Herbert Irving Comprehensive Cancer Vagelos College of Physicians & Surgeons Columbia University (lab head) (1)
Department of Surgery, Charité Universitätsmedizin Berlin (1)
Florence and Herbert Irving Endowed Professor of Medicine Columbia University Irving Medical Center (1)
Helmholtz Zentrum München, Institute of Lung Biology and Disease, Member of the German Center for Lung Research (DZL), Munich, Germany (1)
INSERM U1029, University Bordeaux, Pessac, France (1)
Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France (1)
Mass Spectrometry Facility Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ (1)
Max Planck Institute of Biochemistry Department for Proteomics and Signal Transduction (1)
Professor, Molecular Medicine, Wertheim UF Scripps, USA (1)
Proteomics platform 3P5-Necker, Université Paris Descartes - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris 75014, France. (1)
Research Unit for Precision Regenerative Medicine, Helmholtz Munich, Comprehensive Pneumology Center, Member of the German Center for Lung Research (DZL), Munich, Germany Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany (1)
The Herbert Wertheim UF Scripps Institute for Biomedical Research Innovation and Technology (1)
The Herbert and Jackeline Krieger Klein Alzheimer's Research Center, Brain Health Institute, Rutgers University (1)
Univeristy of Miami Miller School of Medicine (1)

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CodY in Staphylococcus aureus: regulatory link between metabolism and virulence gene expression

CodY is a conserved regulator in gram-positive organisms described to repress metabolic genes mainly involved in nitrogen metabolism but also to control the expression of virulence genes in pathogens. We constructed codY gene-replacement mutants in three unrelated S. aureus strains (Newman, UAMS-1, ...

ORGANISM(S): Staphylococcus aureus subsp. aureus USA300

2008-11-06 | E-GEOD-12340 | biostudies-arrayexpress

Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry

Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives ...

2016-07-27 | MTBLS176 | MetaboLights

Improvements in sleep-disordered breathing during acclimatization to 3800 m and the impact on cognitive function.

Not available

S-EPMC8123551 | biostudies-literature

Human mitochondrial TACO1-FLAG SILAC AP-MS

The prokaryotic translation elongation factor P (EF-P), and the eukaryotic/archeal counterparts eIF5A/aIF5A, are proteins that serve a crucial role in mitigating ribosomal stalling during the translation of specific sequences, notably those containing consecutive proline residues. Although mitochond...

ORGANISM(S): Homo sapiens (Human)

2024-09-06 | PXD051090 | Pride

Comparative analysis of the adaptation of Staphylococcus aureus to internalization by different types of human non-professional phagocytic host cells (NMR assay)

Staphylococcus aureus is a human pathogen that can cause a wide range of diseases. Although formerly regarded as extracellular pathogen, it has been shown that S. aureus can also be internalized by host cells and persist within these cells. In the present study, we comparatively analyzed survival an...

2015-07-01 | MTBLS102 | MetaboLights

Transcriptome analysis of N,C and P limitations in S. coelicolor

A genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon

ORGANISM(S): Streptomyces coelicolor A3(2)

2011-05-01 | E-MAXD-59 | biostudies-arrayexpress

Virulence factors produced by Staphylococcus aureus biofilms have a moonlighting function contributing to biofilm integrity

We comprehensively profiled intracellular and ECM proteomes of S. aureus flow biofilms and complemented these data by metabolic footprint analysis and phenotypic assays. We show that S. aureus biofilms produce high amounts of secreted, moonlighting virulence factors stabilizing the ECM. Mechanistica...

ORGANISM(S): Staphylococcus aureus subsp. aureus NCTC 8325

2019-03-13 | PXD011157 | Pride

Ecm Biofilm Staphylococcus aureus

Molecular structural diversity of mitochondrial cardiolipins

Current strategies used to quantitatively describe the biological diversity of lipids by mass spectrometry are often limited in assessing the exact structural variability of individual molecular species in detail. A major challenge is represented by the extensive isobaric overlap present among lipid...

2021-01-11 | MTBLS636 | MetaboLights

YAGsn2_48rpt

replicate enrichment for soluble proteins; 400-800 m/z; Goo et al., 2003, Mol Cell Proteomics 2(8):511

ORGANISM(S): Halobacterium Nrc-1 (halobacterium)

2006-12-31 | PAe000218 | PeptideAtlas

Ribosomal Assembly Factor Ltv1_L216S Mass Spec

Mass spectrometry data of purified ribosomes in S. cerevisiae containing WT Ltv1 or mutation Ltv1_L216S.

ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast)

2023-10-22 | PXD046239 | Pride

Ribosome Assembly factor Yeast Ltv1

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