Pellet fragmentation

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Proteomics (1467)
Transcriptomics (618)
Metabolomics (94)
Genomics (37)
Unknown (10)
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Organisms

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Allium cepa (2)
Methanococcus maripaludis S2 (2)
Nitrosomonas europaea ATCC 19718 (2)

Organisms

Homo sapiens (4)
Mus musculus (2)
Escherichia coli ATCC 25922 (1)
Porphyromonas gingivalis (1)
Escherichia coli (1)
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Ovis aries (1)

Repository

pride (1453)
biostudies-arrayexpress (641)
MetaboLights (94)
ENA (16)
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jPOST (5)
geo (3)

Tissue

Cell culture (250)
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Cell suspension culture (36)
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Disease

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Squamous cell carcinoma has accession C0007137 in DiseaseStateDatabase NCI_Thesaurus (1)
Internal Carotid Artery Stenosis (NCI Metathesaurus C0340569) has DiseaseStaging Asymptomatic (1)
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Technology Type

Mass Spectrometry (1453)
Shotgun proteomics (824)
Bottom-up proteomics (301)
Data-dependent acquisition (196)
Affinity purification coupled with mass spectrometry proteomics (114)
Mass spectrometry (78)
Gel-based experiment (72)
Data-independent acquisition (57)
SWATH MS (54)
Top-down proteomics (41)
Chemical cross-linking coupled with mass spectrometry proteomics (36)
All-ion fragmentation (25)
SRM/MRM (18)
Mass spectrometry assay (16)
Affinity proteomics (6)
DiaPASEF (5)
HDMSE (4)
Immunopeptidomics (4)
Metaproteomics (4)
NMR spectroscopy (3)
MSE (3)
Mass spectrometry imaging (2)
RNA mass spectrometry (2)
Proteogenomics (1)
Two Dimensional Polyacrylamide Gel Electrophoresis (1)

Instrument Platform

Illumina NovaSeq 6000 (29)
NextSeq 500 (15)
Illumina HiSeq 2000 (13)
Illumina HiSeq 4000 (7)
Illumina NovaSeq X (6)
Illumina HiSeq 2500 (6)
Illumina MiSeq (4)
NextSeq 550 (4)
Illumina Genome Analyzer (3)
GeneChip Scanner 3000 [Affymetrix] (2)
Illumina Genome Analyzer IIx (2)
Axon- GenePix4000B (2)
ScanArray Express HT [PerkinElmer] (2)
Illumina Genome Analyzer II (2)
Scanning hardware (2)
Illumina HiSeq 3000 (2)
Chromium Next GEM Chip G (1)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (1)
10X Genomics Chromium Controller (1)
NextSeq500 (1)
Microarray scanner system (1)
GeneChip Scanner 2500 (1)
Covaris, NEBNext Ultra II DNA library prep kit (1)
Axon Instruments GenePix 4000B scanner (1)
Agilent Scanner (1)
Axon GenePix 4000A scanning hardware (1)
Agilent 2100 Bioanalyzer (1)
ScanArray 4000 [PerkinElmer] (1)
G2500A Hewlett Packard (1)
GenePix 4000A [Axon Instruments] (1)

Publication Date

2025 (271)
2024 (205)
2023 (195)
2022 (186)
2026 (177)
2021 (164)
2020 (130)
2019 (115)
2018 (95)
2015 (85)
2010 (70)
2011 (64)
2016 (63)
2009 (59)
2014 (58)
2017 (57)
2012 (57)
2013 (54)
2008 (35)
2007 (25)
2006 (16)
2005 (13)
2004 (8)
2002 (1)

CHEBI ID

CHEBI:16708 (22)
CHEBI:16335 (22)
CHEBI:7916 (20)
CHEBI:30769 (20)
CHEBI:16027 (18)
CHEBI:17295 (18)
CHEBI:17750 (17)
CHEBI:16750 (17)
CHEBI:17154 (17)
CHEBI:17368 (17)
CHEBI:15891 (16)
CHEBI:17509 (16)
CHEBI:16856 (16)
CHEBI:16015 (16)
CHEBI:30915 (16)
CHEBI:28044 (15)
CHEBI:6650 (15)
CHEBI:16695 (15)
CHEBI:16264 (15)
CHEBI:15741 (15)
CHEBI:18012 (15)
CHEBI:15603 (15)
CHEBI:17895 (15)
CHEBI:16828 (15)
CHEBI:28875 (14)
CHEBI:18050 (14)
CHEBI:18300 (14)
CHEBI:17203 (14)
CHEBI:16977 (14)
CHEBI:17858 (14)

Metabolite Name

Adenine (18)
Pantothenic acid (14)
Adenosine (14)
L-Tyrosine (14)
L-Phenylalanine (14)
L-Tryptophan (13)
Ornithine (12)
Stearic acid (12)
Glutathione (12)
Inosine (12)
Hypoxanthine (12)
L-Alanine (11)
Uracil (11)
Succinic acid (11)
Palmitic acid (11)
Dodecanoic acid (11)
Xanthine (11)
Guanosine (11)
Betaine (10)
Thymine (10)
Maleic acid (10)
Taurine (10)
L-Proline (10)
L-Glutamic acid (10)
Glyceric acid (10)
Malic acid (10)
Uridine (10)
L-Leucine (10)
L-Histidine (9)
Cytosine (9)

First Public Date

2019 (3)
2014 (3)
2024 (2)
2021 (2)
2025 (1)
2023 (1)
2022 (1)
2020 (1)
2017 (1)
2016 (1)

Classification

bacteria (3)

Modification

4-tetrahydrothiazine-3-carboxylic acid (4)
15.99491 (3)
15.994915 (3)
2x(15)N labeled L-lysine (3)
4x(15)N labeled L-arginine (3)
57.02146 (3)
57.021464 (3)
0.984 (2)
4x(2)H labeled dimethylated residue (2)
N6 (2)
-17.026549 (1)
-18.010565 (1)
0.984016 (1)
4 (1)
4'-dihydroxyphenylalanine (1)
42.010565 (1)
43.00581 (1)
58.005479 (1)
6-dioxaoctanediamine derivatized cysteine (1)
79.966331 (1)
N6-dimethyl-L-lysine (1)

Study type

Transcription profiling by array (418)
RNA-seq of coding RNA (96)
Transcription profiling by tiling array (19)
RNA-seq of coding RNA from single cells (15)
ChIP-seq (14)
Comparative genomic hybridization by array (13)
ChIP-chip by array (9)
Methylation profiling by array (9)
Other (8)
ChIP-chip by tiling array (6)
High-throughput sequencing (4)
Methylation profiling by high throughput sequencing (4)
RIP-seq (3)
Single nucleus RNA sequencing (3)
DNA-seq (3)
RNA-seq of total RNA (3)
CLIP-seq (2)
Transcription profiling by high throughput sequencing (1)
Unknown experiment type (1)
Differential (1)
Plant - Two-color microarray (1)
MeDIP-seq (1)
Animal - One-color microarray (1)
Animal - High-throughput sequencing (1)
RNAi profiling by array (1)
RNA-seq of non coding RNA (1)

Release Date

2010 (70)
2011 (64)
2009 (59)
2015 (58)
2012 (57)
2013 (54)
2014 (42)
2008 (35)
2016 (31)
2007 (25)
2006 (17)
2023 (16)
2021 (16)
2017 (16)
2020 (13)
2025 (12)
2005 (12)
2026 (11)
2019 (10)
2024 (9)
2018 (9)
2004 (8)
2022 (6)
2002 (1)

Lab affiliation

University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (23)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (15)
The University of Melbourne (15)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (8)
Max-Planck-Institute for Biology of Ageing Department of Mitochondrial Proteostasis Joseph-Stelzmann-Str. 9b 50931 Cologne (7)
Forest Products Laboratory, Institute for Microbial and Biochemical Sciences, USDA (6)
Department of Biotechnology, TU Delft, The Netherlands (5)
Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany (5)
The University of Manchester (5)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (4)
Department of Biotechnology, Delft University of Technology, The Netherlands. (4)
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden (4)
Department of Neurobiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA (4)
Division of Cell Matrix Biology & Regenerative Medicine (L5) / Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester (4)
Functional Proteomics, ICR (4)
IBCH RAS (4)
North Carolina State University (4)
Aarhus University, Denmark (3)
BIOCEV, First Faculty of Medicine, Charles University, Czech Republic (3)
Cancer Biology Department, Fox Chase Cancer Center, Philadelphia, PA, USA (3)
Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain (3)
Department of Cell Biology, Harvard Medical School, Boston, MA, USA (3)
Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany (3)
Farnusch Kaschani, Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (3)
First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (3)
GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Avenida Lineu Prestes 1374, CEP 05508-000, Sao Paulo, Brazil (3)
Institut für Mikrobiologie, Universität Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald (3)
Institute of Microbiology, Department of Microbial Proteomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany (3)
Institute of Neuronal Cell Biology Technical University of Munich Germany (3)
JGU Mainz (3)

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Dynamics of Pellet Fragmentation and Aggregation in Liquid-Grown Cultures of Streptomyces lividans.

Not available

S-EPMC5958208 | biostudies-literature

Mechanisms of Polyethylene Terephthalate Pellet Fragmentation into Nanoplastics and Assimilable Carbons by Wastewater Comamonas.

Not available

S-EPMC11526368 | biostudies-literature

Surfactant and chaotropic agent assisted sequential extraction/on pellet digestion (SCAD) for enhanced proteomics

As a popular sample preparation approach, Filter-aided sample preparation (FASP) has been widely used in proteomic analysis. However, several limitations have been noted, including sample loss during filtration, repetitive centrifugation steps, and the possibility of breakage of filtration membrane....

ORGANISM(S): Homo sapiens (Human)

2018-10-19 | PXD008967 | Pride

Circulating cell-free DNA fragmentation is a stepwise and conserved process linked to apoptosis.

Not available

S-EPMC10642009 | biostudies-literature

Implications for the mesopelagic microbial gardening hypothesis as determined by experimental fragmentation of Antarctic krill fecal pellets.

Not available

S-EPMC7820144 | biostudies-literature

Electron-Activated Dissociation and Collision-Induced Dissociation Glycopeptide Fragmentation for Improved Glycoproteomics

Protein glycosylation is a critical PTM for the stability and biological function of many proteins, but full characterisation of site-specific glycosylation of proteins remains analytically challenging. Collision induced dissociation (CID) is the most common fragmentation method used in LC-MS/MS wor...

ORGANISM(S): Homo sapiens (Human)

2024-07-04 | PXD050173 | Pride

Cid Glycopeptide Ead Zenotof 7600

Phosphoproteome dynamics of Streptomyces rimosus during submerged growth and antibiotic production

Streptomyces rimosus is an industrial streptomycete, best known as a producer of oxytetracycline, one of the most widely used antibiotics. Despite the significant contribution of Streptomyces species to the pharmaceutical industry, most omics analyses have only been conducted on the model organism, ...

ORGANISM(S): Streptomyces rimosus

2022-08-22 | PXD034565 | Pride

Streptomyces rimosus Phosphoproteome Peptide dimethylation labeling Proteome Pellet fragmentation Oxytetracycline production

Proteomic analysis of Post-COVID Condition: Insights from supernatant and pellet blood fractions

Post-COVID condition (PCC), or long COVID, continues to significantly impact a considerable number of COVID-19 survivors, affecting their quality of life long after the initial infection. In a novel approach utilizing Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) technolog...

ORGANISM(S): Homo sapiens (Human)

2026-02-16 | PXD051740 | Pride

Swath-ms technology Disease severity Blood fractions Proteomics Biomarkers Post-covid condition

Comamonas KF-1 PET degradation

Cellular and extracellular fractions of Comamonas testosteroni KF-1 grown on PET +/- acetate, labeled via diDO-IPTL (Waldbauer et al. 2017 Analytical Chemistry) for protein expression quantitation

ORGANISM(S): Comamonas Testosteroni Kf-1 (ncbitaxon:399795)

MSV000095794 | MassIVE

Transcription profiling of S. cerevisiae (budding yeast) mutants reveals Isc1p plays a key role in hydrogen peroxide resistance and chronological lifespan through modulation of iron levels and programmed cell death

Changes in the transcriptome of Isc1p deficient mutants. The inositolphosphosphingolipid phospholipase C (Isc1p) of Saccharomyces cerevisiae belongs to the family of neutral sphingomyelinases that generates the bioactive sphingolipid ceramide. In this work the role of Isc1p in oxidative stress resis...

ORGANISM(S): Saccharomyces cerevisiae

2008-02-05 | E-MEXP-1136 | biostudies-arrayexpress

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