Protein modifications

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Proteomics (23278)
Unknown (12837)
Transcriptomics (3834)
Genomics (3283)
Metabolomics (250)
Other (235)
Methylation profiling (51)
Models (16)
Multiomics (10)
Genomic (5)
Clinical (1)

Organisms

Homo sapiens (2257)
Mus musculus (1520)
Drosophila melanogaster (427)
Arabidopsis thaliana (367)
Caenorhabditis elegans (235)
Saccharomyces cerevisiae (210)
Rattus norvegicus (106)
Schizosaccharomyces pombe (54)
Danio rerio (49)
Escherichia coli (43)
Bos taurus (37)
Zea mays (31)
cellular organisms (30)
Gallus gallus (27)
Plasmodium falciparum (27)
Oryza sativa (27)
Glycine max (21)
Sus scrofa (20)
Vitis vinifera (18)
Escherichia coli str. K-12 substr. MG1655 (15)
Triticum aestivum (12)
Solea senegalensis (10)
Pan troglodytes (10)
Solanum lycopersicum (10)
Oncorhynchus mykiss (9)
Candida albicans (9)
Chlamydomonas reinhardtii (9)
Enterococcus faecalis (8)
Rhodotorula toruloides (2)
Trypanosoma brucei (2)

Organisms

Homo sapiens (643)
Mus musculus (438)
Arabidopsis thaliana (92)
Drosophila melanogaster (49)
Saccharomyces cerevisiae (49)
Caenorhabditis elegans (19)
Rattus norvegicus (19)
Schizosaccharomyces pombe (13)
Oryza sativa (11)
Plasmodium falciparum (10)
Danio rerio (9)
synthetic construct (8)
Escherichia coli (6)
Xenopus laevis (5)
Sus scrofa (5)
Bos taurus (5)
Triticum aestivum (4)
Lactococcus cremoris subsp. cremoris MG1363 (3)
Saccharolobus islandicus (3)
Neurospora crassa (3)
Macaca mulatta (3)
Glycine max (3)
Toxoplasma gondii (3)
Cryptococcus neoformans H99 (2)
Streptococcus mutans (2)
Trichomonas vaginalis (2)
Trypanosoma brucei (2)
Mycosarcoma maydis (2)
Nannochloropsis oceanica (2)
Aspergillus fumigatus (2)

Repository

pride (20835)
biostudies-arrayexpress (4294)
MassIVE (1900)
ENA (1753)
geo (1228)
iProX (219)
PeptideAtlas (196)
jPOST (160)
MetaboLights (140)
GNPS (110)
EGA (63)
GPMDB (18)
PAXDB (13)
BioModels (12)
LINCS (9)
dbGaP (5)
Cell Collective (4)
NODE (3)
ExpressionAtlas (1)

Tissue

Cell culture (4387)
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Brain (1211)
Permanent cell line cell (702)
Liver (651)
Plant cell (525)
Blood (500)
Blood plasma (497)
Leaf (459)
Fibroblast (434)
Kidney (417)
Heart (383)
Lung (357)
T cell (327)
Breast (73)
Others (69)
Plasma Non-glyco (11)
Digestive System (8)
Male Reproductive System (8)
Female Reproductive System (7)
Large Intestine (6)
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Spleen (3)
Brain (2)
Cell line (1)
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Kidney (1)
Lung (1)
Pancreas (1)

Disease

Colon cancer (304)
Malaria (42)
Normal (13)
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Amyloidosis (1)
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Toxicity (1)
4T1 tumor-bearing (1)
Primary medulloblastoma (1)
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Burkitt's lymphoma (1)
Pseudorabies virus infected (1)
Mild hyperglycemia, liver dysfunction, and renal glycosuria (1)
Spinal muscular atrophy (1)
AIDS-KS, HIV+, nodular (late) stage (1)
Teratozoospermia and infertility (1)
Untreated prostate cancer (1)
Mock infected (1)
Osteosarcoma (1)
These mice have a relatively normal first wave of spermatogenesis but never become fertile. Older animals show increased apoptosis of germ cells, increasing in severity as germ cell stage advances. (1)
Head and neck squamous cell carcinoma (1)
Chronic myelogenous leukemia (1)
Cancer (1)
Renal cell carcinoma (1)
Reference (1)
Chicken Anaemia Virus infected (1)

Technology Type

Mass Spectrometry (20835)
Shotgun proteomics (11351)
Bottom-up proteomics (4321)
Data-dependent acquisition (2531)
Affinity purification coupled with mass spectrometry proteomics (2487)
Gel-based experiment (1407)
Data-independent acquisition (1159)
Top-down proteomics (628)
SWATH MS (465)
Chemical cross-linking coupled with mass spectrometry proteomics (414)
SRM/MRM (188)
Mass spectrometry (112)
All-ion fragmentation (107)
HDMSE (105)
DiaPASEF (96)
Affinity proteomics (73)
MSE (62)
Mass spectrometry assay (24)
GCP (9)
Mass spectrometry (9)
NMR spectroscopy (4)
Illumina HiSeq 2000 (3)
Affymetrix Axiom Genome-Wide ASI 1 Array (1)
Illumina 450k (1)
Illumina ChIP-Sequencing, Illumina MBD-Sequencing, Illumina beadarray, Illumina HiSeq 2500, Illumina MiSeq, Illumina Bisulfite-Sequencing (1)
Illumina HumanOmniExpress-12 v1., Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, Illumina HiSeq 2500 (1)
Illumina MiSeq (1)
Illumina HiSeq 2000, ILLUMINA (1)
NMR spectroscopy assay (1)

Instrument Platform

Illumina NovaSeq 6000 (89)
NextSeq 500 (87)
Illumina HiSeq 2500 (82)
Illumina HiSeq 2000 (82)
Illumina HiSeq 4000 (36)
NextSeq 550 (33)
Illumina MiSeq (29)
HiSeq X Ten (22)
NextSeq 2000 (18)
Illumina NovaSeq X (15)
Illumina Genome Analyzer II (13)
Scanning hardware (13)
Illumina Genome Analyzer IIx (12)
Illumina HiSeq 1500 (10)
GenePix 4000B [Axon Instruments] (5)
Illumina HiSeq 1000 (5)
Conviron controlled environment chamber (4)
AB SOLiD 4 System (4)
GenePix Professional 4200A [Axon Instruments] (4)
GenePix 4000A [Axon Instruments] (4)
DNBSEQ-G400 (4)
MinION (4)
Element AVITI (3)
PromethION (3)
Axon- GenePix4000B (3)
G2565BA DNA microarray scanner [Agilent] (3)
N/A (3)
RNAtag-Seq protocol (Shishkin et al., 2015) (2)
Sequel II (2)
AB SOLiD 5500 (2)

Publication Date

2025 (3632)
2024 (3011)
2022 (2981)
2023 (2894)
2026 (2857)
2021 (2414)
2020 (1839)
2019 (1470)
2018 (1281)
2015 (1038)
2016 (975)
2017 (900)
2013 (891)
2014 (835)
2010 (515)
2011 (477)
2012 (454)
2008 (172)
2009 (155)
2007 (79)
2006 (52)
2005 (27)
2004 (7)
2003 (1)

UNIPROT ID/AC

Q9UQC1 (1)
Q8NB16 (1)
Q9Y572 (1)
P21583 (1)
Q9NQC7 (1)
Q8N5C8 (1)
Q9NYJ8 (1)
Q04864 (1)
Q9BYM8 (1)
Q9H0F6 (1)
Q96EP0 (1)
Q01201 (1)
Q13490 (1)
Q13489 (1)
P31748 (1)
P21580 (1)
Q12933 (1)
Q15628 (1)
Q13546 (1)
Q13131 (1)
P49815 (1)
P42345 (1)
P19438 (1)
P01375 (1)
P35568 (1)
P06213 (1)
P03952 (1)
P07204 (1)
P00488 (1)
P05160 (1)

ENSEMBL ID

ENSG00000170477 (171)
ENSG00000229353 (122)
ENSG00000147251 (120)
ENSG00000204131 (81)
ENSG00000247315 (81)
ENSG00000176092 (36)
ENSG00000003402 (1)
ENSG00000171791 (1)
ENST00000333681.5 (1)
ENSSSCT00065044848.1 (1)
ENST00000371199.8 (1)
ENST00000612899.5 (1)
ENSG00000101966 (1)
ENST00000216797.10 (1)
ENSG00000100906 (1)
ENSG00000118503 (1)

CHEBI ID

CHEBI:17754 (16)
CHEBI:15361 (3)
CHEBI:84651 (2)
CHEBI:88544 (2)
CHEBI:64522 (2)
CHEBI:77086 (2)
CHEBI:84644 (2)
CHEBI:73061 (2)
CHEBI:1 (2)
CHEBI:1879 (2)
CHEBI:58180 (2)
CHEBI:84424 (2)
CHEBI:52381 (2)
CHEBI:53027 (2)
CHEBI:53026 (2)
CHEBI:52385 (2)
CHEBI:52384 (2)
CHEBI:52389 (2)
CHEBI:52615 (2)
CHEBI:52388 (2)
CHEBI:49050 (2)
CHEBI:53040 (2)
CHEBI:52975 (2)
CHEBI:53039 (2)
CHEBI:53035 (2)
CHEBI:53048 (2)
CHEBI:53038 (2)
CHEBI:17309 (2)
CHEBI:53044 (2)
CHEBI:18162 (2)

Metabolite Name

Taurine (16)
Citric acid (14)
Uracil (12)
Adenine (12)
Uridine (12)
L-Phenylalanine (12)
Hypoxanthine (12)
Cytosine (11)
Creatinine (11)
Creatine (11)
Xanthosine (10)
Adenosine (10)
L-Tryptophan (10)
Uric acid (10)
Xanthine (10)
Inosine (10)
L-Threonine (9)
Spermidine (9)
Phenylalanine (9)
Glutamine (9)
L-Serine (9)
Guanosine (9)
L-Methionine (9)
L-Tyrosine (9)
Valine (8)
Betaine (8)
L-Proline (8)
L-Arginine (8)
Succinic acid (8)
L-Asparagine (8)

First Public Date

2025 (243)
2026 (222)
2024 (210)
2023 (208)
2014 (167)
2021 (116)
2022 (105)
2020 (103)
2019 (92)
2018 (68)
2017 (65)
2013 (61)
2015 (47)
2016 (46)

Modelling Approach

Ordinary differential equation model (5)
Constraint-based model (3)
Differential equation model (2)
Petri net (1)

Study status

Terminated (1)

Lab affiliation

University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (121)
EDyP (87)
Head of the Curie Institute Mass Spectrometry Platform (73)
Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States (60)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (43)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (40)
University of Edinburgh (39)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (34)
Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark (32)
Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic (29)
Head of Proteomics (28)
IRCCS Istituto G Gaslini (28)
The Institute of Cancer Research (27)
Functional Proteomics, ICR (26)
OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands (25)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (24)
Imperial College London (23)
Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital (23)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (22)
European Molecular Biology Laboratory (21)
Laboratoire de Spectrométrie de Masse BioOrganique, Analytical Science department, IPHC, CNRS, Strasbourg University, UMR7178, Strasbourg, France (21)
Wellcome Trust Sanger Institute (21)
Institute for Research in Immunology and Cancer, Department of Biochemistry, Department of Chemistry, Université de Montréal, Québec, Canada H3T 1J4 (20)
Utrecht University (20)
Biomolecular characterization unit, Center for Sustainable Resource Science, RIKEN (19)
DZNE Munich, Neuroproteomics, Feodor-Lynen Str. 17, 81377 Munich, Germany (19)
Moffitt Cancer Center Tampa, FL, USA (19)
Chair of Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany (18)
Harvard Medical School (18)
Institute of Molecular Biology (IMB), Mainz, Germany (18)

Keyword

Intra peritonal chemo hyperthermia (1)
Peritoneal carcinomatosis (1)

IsPrivate

False (12)

Submitter Keywords

FROG (3)

Classification

protozoa (21)
bacteria (16)
viruses (8)
fungi (5)
helminths (1)

Modification

4x(15)N labeled L-arginine (51)
2x(15)N labeled L-lysine (46)
N6 (46)
4-tetrahydrothiazine-3-carboxylic acid (39)
15.994915 (38)
N6-dimethyl-L-lysine (31)
57.021464 (27)
42.010565 (24)
Not available (20)
-17.026549 (18)
+3amu) (11)
4x(2)H labeled dimethylated residue (11)
45.029395 (8)
79.966331 (8)
-18.010565 (6)
58.005479 (5)
15.99491 (4)
3x(2)H labeled N6-acetyl-L-lysine (4)
4 (4)
4x(2)H labeled dimethylated L-lysine (4)
57.02146 (4)
71.037114 (4)
10.008269 (3)
56.026215 (3)
6.020129 (3)
6x(2)H labeled dimethylated L-arginine (3)
0.984 (2)
0.984016 (2)
4'-dihydroxyphenylalanine (2)
59.036279 (2)

Study type

Transcription profiling by array (1396)
ChIP-seq (906)
RNA-seq of coding RNA (527)
ChIP-chip by tiling array (477)
Methylation profiling by high throughput sequencing (144)
Other (111)
RNA-seq of non coding RNA (103)
Methylation profiling by array (100)
Comparative genomic hybridization by array (74)
ChIP-chip by array (72)
RNA-seq of coding RNA from single cells (36)
Genotyping by high throughput sequencing (32)
Unknown experiment type (29)
DNA-seq (28)
ATAC-seq (25)
RNA-seq of total RNA (25)
Transcription profiling by tiling array (20)
Cell line - High-throughput sequencing (19)
MicroRNA profiling by array (17)
CUT&RUN (16)
High-throughput sequencing (13)
RIP-seq (10)
Proteomic profiling by array (10)
Animal - High-throughput sequencing (8)
CLIP-seq (8)
Bisulfite-seq (8)
MicroRNA profiling by high throughput sequencing (7)
Hi-C (7)
Plant - High-throughput sequencing (6)
Transcription profiling by SAGE (5)

Release Date

2023 (1222)
2022 (1221)
2025 (1199)
2021 (1186)
2013 (1171)
2015 (1049)
2014 (1042)
2024 (1034)
2020 (989)
2016 (899)
2012 (823)
2019 (806)
2011 (789)
2018 (785)
2010 (758)
2017 (755)
2009 (372)
2008 (350)
2026 (201)
2007 (160)
2006 (118)
2005 (73)
2004 (39)
2003 (27)
2002 (23)
2001 (14)
2000 (7)
1998 (7)
1999 (5)
1997 (2)

Location

France (1)

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Identification of the modifications in artificial E. coli rRNAs

Ribosome biogenesis is pivotal in the self-replication of life. In Escherichia coli, three ribosomal RNAs and 54 ribosomal proteins are synthesized and subjected to cooperative hierarchical assembly facilitated by numerous accessory factors. Realizing ribosome biogenesis in vitro is a critical miles...

2024-12-09 | MTBLS7425 | MetaboLights

The Bardet-Biedl protein Bbs1 controls photoreceptor outer segment protein and lipid composition

Summary

Primary cilia are key sensory organelles whose dysfunction leads to ciliopathy disorders such as Bardet-Biedl syndrome (BBS). Retinal degeneration is common in ciliopathies, since the outer segments (OSs) of photoreceptors are highly specialized primary cilia. BBS...

2022-02-18 | MTBLS4013 | MetaboLights

Multiomics analysis of residual feed intake regulation in calves by intestinal microbiota-mediated epigenetic modifications

Feed efficiency is a critical trait affecting the economic profitability and environmental sustainability of livestock production. Residual Feed Intake (RFI), as a key metric for feed efficiency, effectively reflects differences in energy utilization for maintenance and production. This study aims t...

2026-04-20 | MTBLS14315 | MetaboLights

Fatty acid transport protein 4 is required for incorporation of saturated ultralong-chain fatty acids into epidermal ceramides and monoacylglycerols

Fatty acid transport protein 4 (FATP4) is an acyl-CoA synthetase that is required for normal permeability barrier in mammalian skin. FATP4 (SLC27A4) mutations cause ichthyosis prematurity syndrome, a nonlethal disorder. In contrast, Fatp4^-/- mice die neonatally from a defective barrier. H...

2021-07-15 | MTBLS1138 | MetaboLights

Posttranslational modification analysis of Histone H3t

Comprehensive posttranslational modifications in the testis-specific histone variant H3t protein validated in tagged knock-in mice.

ORGANISM(S): Mus Musculus (mouse)

2024-09-13 | PXD052428 | JPOST Repository

Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip.

A global view of PML-RAR? transcriptional functions was obtained by genome-wide binding and chromatin modification analyses, combined with genome wide expression data. Complete Abstract: The translocation t(15;17) generates the chimeric PML-RAR? transcription factor that is the initiating event of ...

ORGANISM(S): Homo sapiens

2008-09-06 | E-GEOD-12641 | biostudies-arrayexpress

Chemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans

Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs...

ORGANISM(S): Homo sapiens

2015-10-31 | E-GEOD-66224 | biostudies-arrayexpress

Fine mapping of posttranslational modifications of the linker histone H1 from Drosophila melanogaster.

Not available

S-EPMC2212714 | biostudies-literature

Regulation of alternative splicing by histone modifications

Alternative splicing of pre-mRNA is a prominent mechanism to generate protein diversity, yet its regulation is poorly understood. Here, we demonstrate a direct role for histone modifications in alternative splicing. We find distinctive histone modification signatures which correlate with splicing ou...

ORGANISM(S): Homo sapiens

2010-02-10 | E-GEOD-19373 | biostudies-arrayexpress

AUTO-SP: automated sample preparation for analyzing proteins and protein modifications

Liquid chromatography (LC) tandem mass spectrometry (MS/MS) is one of the widely used proteomic techniques to study the alterations occurred at protein level as well as post-translation modifications (PTMs) of proteins that are relevant to different physiological or pathological statuses. The mass s...

ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human)

2026-03-16 | PXD064088 | Pride

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