Integrative top-down proteomics

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Proteomics (53)
Unknown (7)

Organisms

Schizophyllum commune H4-8 (51)
Mycobacterium tuberculosis SP7 (51)
Oryza sativa Japonica Group (51)
Crotalus durissus terrificus (51)
Eriocheir sinensis (51)
Candidatus Endoriftia persephonae (51)
Mycobacterium tuberculosis SP10 (51)
Mycobacterium tuberculosis SP13 (51)
Cotesia typhae (51)
Mycobacterium tuberculosis SP22 (51)
Cepaea nemoralis (51)
Enterobacter ludwigii (51)
Corynebacterium diphtheriae bv. mitis str. ISS 3319 (51)
Olea europaea (51)
Chlamydomonas reinhardtii (51)
Lama (51)
Planorbella pilsbryi (51)
Wolbachia sp. wMelPop (51)
Pyricularia oryzae P131 (51)
Enterococcus mundtii CRL35 (51)
Pongo pygmaeus (51)
Oncorhynchus tshawytscha (51)
Pseudomonas canadensis (51)
Strongylocentrotus purpuratus (51)
Influenza A virus (A/California/04/2009(H1N1)) (51)
Salmonella enterica subsp. enterica serovar Typhimurium (51)
Homo (51)
Bradyrhizobium diazoefficiens (51)
Streptococcus pyogenes STAB901 (51)
Vipera anatolica senliki (1)

Repository

pride (51)
MassIVE (2)

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Disease

Alzheimer's disease (3)
Breast cancer (3)
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Coccidioidomycosis (1)
Diastolic heart failure (1)
Alport syndrome (1)
Obesity (1)
Prostate adenocarcinoma (1)
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Cardiovascular system disease (1)
Tuberculosis (1)
Malignant neoplasm of ovary (1)
Type 2 diabetes mellitus (1)
Disease free (1)
Colon cancer (1)

Technology Type

Mass Spectrometry (51)
Top-down proteomics (22)
Shotgun proteomics (19)
Data-dependent acquisition (6)
Bottom-up proteomics (4)
Affinity purification coupled with mass spectrometry proteomics (3)
Chemical cross-linking coupled with mass spectrometry proteomics (2)
SWATH MS (1)
Data-independent acquisition (1)
SRM/MRM (1)
Gel-based experiment (1)

Instrument Platform

LTQ Orbitrap Velos (1)
LTQ Orbitrap XL (1)
Q Exactive Plus (1)

Publication Date

2025 (10)
2026 (7)
2024 (6)
2023 (6)
2021 (6)
2022 (5)
2020 (4)
2019 (4)
2018 (3)
2017 (1)
2016 (1)

Release Date

2024 (2)
2020 (2)
2023 (1)
2019 (1)
2017 (1)

Lab affiliation

Director, Centre for Proteome Research Department of Biochemistry & Systems Biology Institute of Systems, Molecular & Integrative Biology University of Liverpool Crown Street, Liverpool L69 7ZB +44 151 795 4424 (2)
Massachusetts Institute of Technology, Department of Biological Engineering, David H Koch Institute for Integrative Cancer Research (2)
Centre for Proteome Research G44, Biosciences Building| Institute of Systems, Molecular and Integrative Biology University of Liverpool Crown Street | Liverpool | L69 7ZB +44 151 794 4312 (2)
Proteomics Unit Navarrabiomed, Pamplona, Spain (2)
Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain (2)
Department of Biological Engineering, Massachusetts Institute of Technology & Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (1)
Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands. & Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands. (1)
5Department of Biotechnology, Graduate School of Engineering, Osaka University (1)
The University of Tennessee Health Science Center (1)
Department of Biological Engineering, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA (lab head) (1)
Khon Kaen University National Phenome Institute, Regional Science Park Northeast 1, Khon Kaen University, Khon Kaen, 40002, Thailand (1)
Utrecht University / Pharmaceutical Sciences Biomolecular Mass Spectrometry and Proteomics Padualaan 8 , 3584 CH Utrecht (1)
Laboratory of Regenerative and Movement Biology, Dept. of Health Sciences and Technology ETH Zurich, Schorenstrasse 16, 8603 Schwerzenbach, Switzerland (1)
Proteomics, Lipidomics and Metabolomics Core Facility, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia (1)
Nanjing Agricultural University, Binjiang Campus (1)
Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA 02139, Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA 02142 USA, Center for Precision Cancer Medicine Massachusetts Institute of Technnology Cambridge MA 02142 USA (1)
Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120, Halle/Saale, Germany Institute of Chemical Biology, National Hellenic Research Foundation, Athens, 11635, Greece (1)
Faculty of Health School of Biomedical Sciences Queensland University of Technology (1)
Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University (1)
Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary Department of Chemistry, University of Calgary (1)
Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea (1)
Koch Institute for Integrative Cancer Research Center for Precision Cancer Medicine Department of Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, USA (1)
Erasmus MC, dept. Medical Oncology, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands (1)
Department of Biological Sciences, University of Delaware, USA (1)
Department of molecular and integrative physiology, university of michigan, ann arbor MI 48109 (1)
Department of Molecular Physiology and Cell Signalling Institute of Systems, Molecular and Integrative Biology University of Liverpool (1)
Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, P. R. China (1)
Department of Thoracic Surgery and Lung Transplantation, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China (1)
Division of Chemical and Systems Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease and Molecular Medicine, Faculty of Health Science, University of Cape Town, South Africa. (1)
Department of Molecular Cell Biology, Institute of Biochemistry, Splaiul Independentei 296, 060031 Bucharest 17, Romania (1)

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Optimized Proteome Reduction for Integrative Top-Down Proteomics.

Not available

S-EPMC10059017 | biostudies-literature

Protein ‘Purity’, Proteoforms, and the Albuminome: Critical Observations on Proteome and Systems Complexity

The identification of effective, selective biomarkers and therapeutics is dependent on truly deep, comprehensive analysis of proteomes at the proteoform level. Using bovine serum albumin (BSA) isolated by two different protocols, cold ethanol fractionation (CEF) and heat shock fractionation (HSF), t...

ORGANISM(S): Bos taurus (Bovine)

2024-12-07 | PXD056316 | Pride

An integrative proteotranscriptomics approach reveals new ADAM9 substrates and downstream pathways

An integrative proteotranscriptomics approach to uncover the transcriptional and post-transcriptional targets of the disintegrin metalloproteinase ADAM9, a sheddase that has been implicated in solid tumors, autoimmunity, inflammatory diseases and COVID-19. This systematic approach revealed signaling...

ORGANISM(S): Homo sapiens (Human)

2026-04-13 | PXD059109 | Pride

Multiomics Metalloproteinase Proteotranscriptomics Integration Adam9 Target identification

How paired PSII-LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by integrative structural mass-spectrometry

Photosynthesis drives all life on Earth by exploiting solar energy to split water molecules through the Photosystem (PS) II enzyme. In plant thylakoid membranes, PSII binds a modular set of light harvesting complexes (LHCII) to form different types of PSII-LHCII supercomplex (PSII-LHCIIsc). Plant PS...

ORGANISM(S): Pisum sativum (Garden pea)

2020-03-19 | PXD017382 | Pride

Plant proteomics Top-down rp-lc-ms/ms Acetylation Dsso Psii Edc Photosystem Cx-ms Crosslinking Chlorophyll-binding proteins

An integrative proteomic approach during Alzheimer’s disease progression in Tau PS19 mice

Alzheimer's disease (AD) is a slowly progressive neurodegenerative disease associated with cognitive, functional, and behavioral impairments characterized by the progressive accumulation of extracellular amyloid-beta plaques and intracellular neurofibrillary tangles of hyperphosphorylated tau protei...

ORGANISM(S): Mus musculus (Mouse)

2026-06-15 | PXD066515 | Pride

Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with acid guanidinium thiocyanate-phenol-chloroform

Acid guanidinium thiocyanate, phenol and chloroform extraction (AGPC) is a commonly used procedure to extract RNA from fresh frozen tissues and cell lines. In addition, DNA and proteins can be recovered, which makes AGPC an attractive source for integrative analysis on tissues of which little materi...

ORGANISM(S): Homo sapiens (Human)

2016-06-24 | PXD001533 | Pride

Proteogenomics Acid guanidinium phenol-chloroform Shotgun proteomics Rna bee Breast cancer Sample preparation

Brain proteomics in Alzheimer's disease

Quantify region-dependent fluctuations on a proteome-wide scale, performing integrative analysis of the proteome and phosphoproteome across AD stages in EC and FC.

ORGANISM(S): Homo sapiens (Human)

2022-02-16 | PXD021645 | Pride

Proteomics Brain Phosphoproteomics

Human HFpEF Myocardial Proteomics

Background: Heart failure with preserved ejection fraction (HFpEF) constitutes more than half of all heart failure but has few effective therapies. Recent human myocardial transcriptomics and metabolomics have revealed major differences between HFpEF, HF with reduced EF (HFrEF), and controls. How th...

ORGANISM(S): Homo sapiens (Human)

2024-03-05 | PXD045677 | Pride

Proteomics Myocardium Obesity Molecular medicine Heart disease Human

Protein "purity," proteoforms, and the albuminome: critical observations on proteome and systems complexity.

Not available

S-EPMC11666697 | biostudies-literature

PEPPI-MS: Polyacrylamide-Gel-Based Prefractionation for Analysis of Intact Proteoforms and Protein Complexes by Mass Spectrometry.

Not available

S-EPMC8141340 | biostudies-literature

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