Shotgun discovery proteomics

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Proteomics (9919)
Unknown (132)
Transcriptomics (11)
Genomics (3)
Other (2)

Organisms

Allexis (9861)
Homo sapiens (9861)
Mus musculus (9861)
Rattus norvegicus (9861)
Shigella (9861)
Shigella flexneri (9861)
Arabidopsis thaliana (9860)
Listeria monocytogenes (9860)
Saccharomyces cerevisiae (9860)
Schizosaccharomyces pombe (9859)
Escherichia coli (9858)
Staphylococcus aureus (9858)
Entamoeba histolytica HM-1:IMSS-A (9857)
Solanum tuberosum (9857)
Medicago truncatula (9856)
Sinorhizobium meliloti BL225C (9856)
Sus scrofa domesticus (9856)
Zea mays (9855)
Meleagris gallopavo (9853)
Methylohalobius crimeensis 10Ki (9853)
Bos taurus (9852)
Homo sapiens (22)
Mus musculus (4)
Bartonella henselae (2)
Solanum lycopersicum (1)
Bos taurus (1)
Saccharomyces cerevisiae (1)
Haloferax volcanii DS2 (1)
Schistosoma mansoni (1)
Fusarium sinicum (1)

Organisms

Bartonella henselae (1)
Homo sapiens (1)

Repository

pride (9862)
MassIVE (28)
biostudies-arrayexpress (10)
PAXDB (9)
iProX (8)
jPOST (7)
PanoramaPublic (5)
geo (2)
GPMDB (2)
ENA (2)

Tissue

Cell culture (2065)
Epithelial cell (586)
Brain (580)
Liver (334)
Permanent cell line cell (331)
Blood plasma (283)
Plant cell (255)
Leaf (238)
Blood (236)
Heart (216)
Kidney (210)
Fibroblast (207)
Lung (204)
Whole body (173)
Cell suspension culture (152)
Macrophage (151)
T cell (143)
Blood cell (132)
Blood serum (132)
Colon (125)
Hepatocyte (125)
B cell (119)
Skin (109)
Root (106)
Stem cell (103)
Bone marrow (99)
HeLa cell (93)
Primary cell (92)
Embryo (91)
Embryonic stem cell (85)

Disease

Disease free (243)
Breast cancer (232)
Colon cancer (128)
Acute leukemia (105)
Cardiovascular system disease (84)
Alzheimer's disease (82)
Cervix carcinoma (71)
Malignant neoplasm of ovary (55)
Prostate adenocarcinoma (49)
Melanoma (48)
Wounds and Injuries (48)
Lymphoma (45)
Parkinson's disease (45)
Lung cancer (43)
Type 2 diabetes mellitus (43)
Brain cancer (37)
COVID-19 (34)
Non-small cell lung carcinoma (33)
Hepatocellular carcinoma (31)
Plasmodium falciparum malaria (31)
Amyotrophic lateral sclerosis (29)
Pancreatic ductal adenocarcinoma (27)
Glioblastoma (25)
Brain glioblastoma multiforme (23)
Huntington Disease (23)
Neuroblastoma (21)
Pancreatic cancer (21)
Lung adenocarcinoma (20)
Malaria (20)
Not Available (2)

Technology Type

Mass Spectrometry (9862)
Shotgun proteomics (9591)
Affinity purification coupled with mass spectrometry proteomics (566)
Gel-based experiment (320)
SWATH MS (193)
Bottom-up proteomics (165)
Data-dependent acquisition (95)
SRM/MRM (95)
Top-down proteomics (63)
HDMSE (52)
Chemical cross-linking coupled with mass spectrometry proteomics (48)
All-ion fragmentation (17)
Data-independent acquisition (17)
Mass spectrometry imaging (8)
MSE (7)
Metaproteomics (5)
Affinity proteomics (3)
Gel-free quantification method (1)
Glycoproteomics (1)

Instrument Platform

LTQ Orbitrap Velos (5)
LTQ Orbitrap Elite (4)
LTQ Orbitrap (3)
Q Exactive (3)
Illumina HiSeq 2500 (2)
Illumina HiSeq 2000 (2)
Instrument (2)
6520A Quadrupole Time-of-Flight LC/MS (2)
Orbitrap Fusion (2)
TSQ Quantiva (2)
Affymetrix Gene Atlas System (1)
Agilent 2100 Bioanalyzer (1)
NextSeq 500 (1)
LTQ Velos (1)
LTQ XL ETD (1)
MS:1000031 (1)
MS:1000490 (1)
Orbitrap Fusion Lumos (1)
Orbitrap Q Exactive HF (1)
Q Exactive HF (1)
Q Exactive Plus (1)
Q-exactive (1)
QSTAR XL (1)
LTQ-FT2 (1)

Publication Date

2022 (1572)
2023 (1494)
2021 (1405)
2020 (1042)
2019 (927)
2024 (859)
2018 (786)
2017 (489)
2025 (438)
2016 (387)
2015 (250)
2026 (162)
2014 (92)
2013 (22)
2010 (2)
2012 (2)

UNIPROT ID/AC

10090.ENSMUSP00000053997 (3)
10090.ENSMUSP00000072521 (3)
10090.ENSMUSP00000076447 (3)
10090.ENSMUSP00000079944 (3)
10090.ENSMUSP00000085580 (3)
10090.ENSMUSP00000089293 (3)
10090.ENSMUSP00000095287 (3)
10090.ENSMUSP00000105709 (3)
10090.ENSMUSP00000106336 (3)
10090.ENSMUSP00000108837 (3)
10090.ENSMUSP00000112386 (3)
10090.ENSMUSP00000117461 (3)
10090.ENSMUSP00000123410 (3)
10090.ENSMUSP00000123798 (3)
10090.ENSMUSP00000124509 (3)
10090.ENSMUSP00000124523 (3)
10090.ENSMUSP00000124578 (3)
10090.ENSMUSP00000125590 (3)
10090.ENSMUSP00000125806 (3)
10090.ENSMUSP00000127198 (3)
10090.ENSMUSP00000129930 (3)
10090.ENSMUSP00000131850 (3)
10090.ENSMUSP00000132102 (3)
10090.ENSMUSP00000135978 (3)
10090.ENSMUSP00000136172 (3)
10090.ENSMUSP00000136301 (3)
10090.ENSMUSP00000136544 (3)
10090.ENSMUSP00000137171 (3)
10090.ENSMUSP00000137244 (3)
10090.ENSMUSP00000137310 (3)

First Public Date

2017 (1)
2013 (1)

Classification

bacteria (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (21)
2x(15)N labeled L-lysine (18)
4x(15)N labeled L-arginine (17)
15.994915 (13)
N6-dimethyl-L-lysine (13)
Not available (13)
57.021464 (12)
N6 (12)
4x(2)H labeled dimethylated residue (9)
42.010565 (8)
-17.026549 (7)
-18.010565 (6)
15.99491 (4)
4x(2)H labeled dimethylated L-lysine (4)
57.02146 (4)
+3amu) (3)
0.984 (2)
4 (2)
45.029395 (2)
58.005479 (2)
6x(2)H labeled dimethylated L-arginine (2)
79.966331 (2)
0.984016 (1)
10.008269 (1)
14.01565 (1)
19.989829 (1)
1x(15)N labeled L-valine (1)
203.0794 (1)
28.0313 (1)
3'' (1)

Study type

RNA-seq of coding RNA (8)
ChIP-seq (1)
Transcription profiling by array (1)

Release Date

2021 (16)
2017 (12)
2014 (11)
2013 (11)
2022 (11)
2018 (10)
2023 (9)
2019 (9)
2025 (8)
2016 (8)
2015 (8)
2020 (8)
2011 (6)
2024 (5)
2009 (4)
2012 (2)
2026 (1)
2010 (1)
2007 (1)
2005 (1)

Lab affiliation

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (83)
EDyP (46)
University of Victoria (38)
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 (26)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (24)
Laboratoire de Spectrométrie de Masse BioOrganique, Analytical Science department, IPHC, CNRS, Strasbourg University, UMR7178, Strasbourg, France (18)
Instituto de Investigaciones Sanitarias de Santiago de Compostela (17)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (16)
The University of Melbourne (16)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (15)
Institute of Molecular Biology (IMB), Mainz, Germany (14)
North Carolina State University (13)
Pacific Northwest National Laboratory (13)
Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital (13)
The University of Sydney (12)
University of Washington (12)
CRUK Beatson Institute (11)
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK (11)
Professor of Genomic Evolution, School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin Belfield Dublin 4 (11)
Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (11)
Associate Member Developmental Neurobiology St. Jude Children's Research Hospital (10)
Department of Biotechnology, Delft University of Technology, The Netherlands. (10)
Harvard Medical School (10)
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205 USA (10)
College of Animal Sciences, Zhejiang University, Hangzhou, P. R. China (9)
Head of the Curie Institute Mass Spectrometry Platform (9)
Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA (9)
Universität Greifswald Institut für Pharmazie, AG Pharmazeutische Biotechnologie Greifswald, Germany (9)
Brigham and Women's Hospital, Harvard Medical School (8)
Cambridge Institute for Medical Research, University of Cambridge (8)

Tags

xref:PubMed:23878158 (1)
xref:PubMed:29141959 (1)
pathogen (1)
pathogen:bacterium (1)

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Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.

Not available

S-EPMC4533616 | biostudies-literature

Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster.

Not available

S-EPMC4732435 | biostudies-literature

A Digital Pathology-Based Shotgun-Proteomics Approach to Biomarker Discovery in Colorectal Cancer.

Not available

S-EPMC6939342 | biostudies-literature

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics.

Not available

S-EPMC7261821 | biostudies-literature

Shotgun proteomics to characterize wastewater proteins.

Not available

S-EPMC10579522 | biostudies-literature

Directed shotgun proteomics guided by RNA-Seq identifies a complete expressed prokaryotic proteome

Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and ...

ORGANISM(S): Bartonella henselae

2013-04-23 | E-GEOD-44564 | biostudies-arrayexpress

ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects.

Not available

S-EPMC4630118 | biostudies-literature

Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics.

Not available

S-EPMC6398204 | biostudies-literature

Directed shotgun proteomics guided by RNA-Seq identifies a complete expressed prokaryotic proteome

ORGANISM(S): Bartonella henselae

2013-04-23 | GSE44564 | GEO

Robust determination of differential abundance in shotgun proteomics using nonparametric statistics.