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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of April 9, 2023. |
#Lipton MS, <i>et al.</i> (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [https://pubmed.ncbi.nlm.nih.gov/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | #Lipton MS, <i>et al.</i> (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [https://pubmed.ncbi.nlm.nih.gov/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Tam V, <i>et al.</i> (2020) "DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/33382035 33382035]; doi: [https://dx.doi.org/10.7554/eLife.64940 10.7554/eLife.64940]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33382035 263]. | #Tam V, <i>et al.</i> (2020) "DIPPER, a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics." <i>Elife</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/33382035 33382035]; doi: [https://dx.doi.org/10.7554/eLife.64940 10.7554/eLife.64940]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33382035 263]. | ||
#Barbosa P, <i>et al.</i> (2021) "SCF-Fbxo42 promotes synaptonemal complex assembly by downregulating PP2A-B56." <i>J Cell Biol</i> <b>220</b>(2):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33382409 33382409]; doi: [https://dx.doi.org/10.1083/jcb.202009167 10.1083/jcb.202009167]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33382409 14]. | #Barbosa P, <i>et al.</i> (2021) "SCF-Fbxo42 promotes synaptonemal complex assembly by downregulating PP2A-B56." <i>J Cell Biol</i> <b>220</b>(2):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33382409 33382409]; doi: [https://dx.doi.org/10.1083/jcb.202009167 10.1083/jcb.202009167]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33382409 14]. | ||
- | #Subbannayya Y, <i>et al.</i> (2020) "The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function." <i>Int J Mol Sci</i> <b>22</b>(1):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33383959 33383959]; doi: [https://dx.doi.org/10.3390/ijms22010275 10.3390/ijms22010275]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33383959 | + | #Subbannayya Y, <i>et al.</i> (2020) "The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function." <i>Int J Mol Sci</i> <b>22</b>(1):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33383959 33383959]; doi: [https://dx.doi.org/10.3390/ijms22010275 10.3390/ijms22010275]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33383959 15]. |
#Dietze R, <i>et al.</i> (2021) "Phosphoproteomics identify arachidonic-acid-regulated signal transduction pathways modulating macrophage functions with implications for ovarian cancer." <i>Theranostics</i> <b>11</b>(3):1377–1395; PMID: [https://pubmed.ncbi.nlm.nih.gov/33391540 33391540]; doi: [https://dx.doi.org/10.7150/thno.52442 10.7150/thno.52442]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33391540 63]. | #Dietze R, <i>et al.</i> (2021) "Phosphoproteomics identify arachidonic-acid-regulated signal transduction pathways modulating macrophage functions with implications for ovarian cancer." <i>Theranostics</i> <b>11</b>(3):1377–1395; PMID: [https://pubmed.ncbi.nlm.nih.gov/33391540 33391540]; doi: [https://dx.doi.org/10.7150/thno.52442 10.7150/thno.52442]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33391540 63]. | ||
#Khan MJ, <i>et al.</i> (2021) "Why Inclusion Matters for Alzheimer's Disease Biomarker Discovery in Plasma." <i>J Alzheimers Dis</i> <b>79</b>(3):1327–1344; PMID: [https://pubmed.ncbi.nlm.nih.gov/33427747 33427747]; doi: [https://dx.doi.org/10.3233/JAD-201318 10.3233/JAD-201318]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33427747 25]. | #Khan MJ, <i>et al.</i> (2021) "Why Inclusion Matters for Alzheimer's Disease Biomarker Discovery in Plasma." <i>J Alzheimers Dis</i> <b>79</b>(3):1327–1344; PMID: [https://pubmed.ncbi.nlm.nih.gov/33427747 33427747]; doi: [https://dx.doi.org/10.3233/JAD-201318 10.3233/JAD-201318]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33427747 25]. | ||
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#Gastaldello A, <i>et al.</i> (2021) "The immunopeptidomes of two transmissible cancers and their host have a common, dominant peptide motif." <i>Immunology</i> <b>163</b>(2):169–184; PMID: [https://pubmed.ncbi.nlm.nih.gov/33460454 33460454]; doi: [https://dx.doi.org/10.1111/imm.13307 10.1111/imm.13307]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33460454 9]. | #Gastaldello A, <i>et al.</i> (2021) "The immunopeptidomes of two transmissible cancers and their host have a common, dominant peptide motif." <i>Immunology</i> <b>163</b>(2):169–184; PMID: [https://pubmed.ncbi.nlm.nih.gov/33460454 33460454]; doi: [https://dx.doi.org/10.1111/imm.13307 10.1111/imm.13307]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33460454 9]. | ||
#Lobato-Gil S, <i>et al.</i> (2021) "Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation." <i>Cell Rep</i> <b>34</b>(3):108635; PMID: [https://pubmed.ncbi.nlm.nih.gov/33472076 33472076]; doi: [https://dx.doi.org/10.1016/j.celrep.2020.108635 10.1016/j.celrep.2020.108635]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33472076 24]. | #Lobato-Gil S, <i>et al.</i> (2021) "Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation." <i>Cell Rep</i> <b>34</b>(3):108635; PMID: [https://pubmed.ncbi.nlm.nih.gov/33472076 33472076]; doi: [https://dx.doi.org/10.1016/j.celrep.2020.108635 10.1016/j.celrep.2020.108635]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33472076 24]. | ||
+ | #Floyd BM, <i>et al.</i> (2021) "Systematic Identification of Protein Phosphorylation-Mediated Interactions." <i>J Proteome Res</i> <b>20</b>(2):1359–1370; PMID: [https://pubmed.ncbi.nlm.nih.gov/33476154 33476154]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00750 10.1021/acs.jproteome.0c00750]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33476154 308]. | ||
#Huang KK, <i>et al.</i> (2021) "Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer." <i>Genome Biol</i> <b>22</b>(1):44; PMID: [https://pubmed.ncbi.nlm.nih.gov/33482911 33482911]; doi: [https://dx.doi.org/10.1186/s13059-021-02261-x 10.1186/s13059-021-02261-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33482911 80]. | #Huang KK, <i>et al.</i> (2021) "Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer." <i>Genome Biol</i> <b>22</b>(1):44; PMID: [https://pubmed.ncbi.nlm.nih.gov/33482911 33482911]; doi: [https://dx.doi.org/10.1186/s13059-021-02261-x 10.1186/s13059-021-02261-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33482911 80]. | ||
#Osório H, <i>et al.</i> (2021) "Proteomics Analysis of Gastric Cancer Patients with Diabetes Mellitus." <i>J Clin Med</i> <b>10</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33494396 33494396]; doi: [https://dx.doi.org/10.3390/jcm10030407 10.3390/jcm10030407]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33494396 40]. | #Osório H, <i>et al.</i> (2021) "Proteomics Analysis of Gastric Cancer Patients with Diabetes Mellitus." <i>J Clin Med</i> <b>10</b>(3):; PMID: [https://pubmed.ncbi.nlm.nih.gov/33494396 33494396]; doi: [https://dx.doi.org/10.3390/jcm10030407 10.3390/jcm10030407]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33494396 40]. | ||
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#Swaney DL, <i>et al.</i> (2021) "A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity." <i>Science</i> <b>374</b>(6563):eabf2911; PMID: [https://pubmed.ncbi.nlm.nih.gov/34591642 34591642]; doi: [https://dx.doi.org/10.1126/science.abf2911 10.1126/science.abf2911]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34591642 551]. | #Swaney DL, <i>et al.</i> (2021) "A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity." <i>Science</i> <b>374</b>(6563):eabf2911; PMID: [https://pubmed.ncbi.nlm.nih.gov/34591642 34591642]; doi: [https://dx.doi.org/10.1126/science.abf2911 10.1126/science.abf2911]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34591642 551]. | ||
#Stieglitz F, <i>et al.</i> (2021) "The Binary Toxin of <i>Clostridioides difficile</i> Alters the Proteome and Phosphoproteome of HEp-2 Cells." <i>Front Microbiol</i> <b>12</b>:725612; PMID: [https://pubmed.ncbi.nlm.nih.gov/34594315 34594315]; doi: [https://dx.doi.org/10.3389/fmicb.2021.725612 10.3389/fmicb.2021.725612]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34594315 57]. | #Stieglitz F, <i>et al.</i> (2021) "The Binary Toxin of <i>Clostridioides difficile</i> Alters the Proteome and Phosphoproteome of HEp-2 Cells." <i>Front Microbiol</i> <b>12</b>:725612; PMID: [https://pubmed.ncbi.nlm.nih.gov/34594315 34594315]; doi: [https://dx.doi.org/10.3389/fmicb.2021.725612 10.3389/fmicb.2021.725612]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34594315 57]. | ||
+ | #Krieg L, <i>et al.</i> (2022) "Multiomics reveal unique signatures of human epiploic adipose tissue related to systemic insulin resistance." <i>Gut</i> <b>71</b>(11):2179–2193; PMID: [https://pubmed.ncbi.nlm.nih.gov/34598978 34598978]; doi: [https://dx.doi.org/10.1136/gutjnl-2021-324603 10.1136/gutjnl-2021-324603]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34598978 270]. | ||
#Ross SH, <i>et al.</i> (2021) "Quantitative Analyses Reveal How Hypoxia Reconfigures the Proteome of Primary Cytotoxic T Lymphocytes." <i>Front Immunol</i> <b>12</b>:712402; PMID: [https://pubmed.ncbi.nlm.nih.gov/34603285 34603285]; doi: [https://dx.doi.org/10.3389/fimmu.2021.712402 10.3389/fimmu.2021.712402]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34603285 6]. | #Ross SH, <i>et al.</i> (2021) "Quantitative Analyses Reveal How Hypoxia Reconfigures the Proteome of Primary Cytotoxic T Lymphocytes." <i>Front Immunol</i> <b>12</b>:712402; PMID: [https://pubmed.ncbi.nlm.nih.gov/34603285 34603285]; doi: [https://dx.doi.org/10.3389/fimmu.2021.712402 10.3389/fimmu.2021.712402]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34603285 6]. | ||
+ | #Tian F, <i>et al.</i> (2021) "Proteomic Response of Rat Pituitary Under Chronic Mild Stress Reveals Insights Into Vulnerability and Resistance to Anxiety or Depression." <i>Front Genet</i> <b>12</b>:751999; PMID: [https://pubmed.ncbi.nlm.nih.gov/34603401 34603401]; doi: [https://dx.doi.org/10.3389/fgene.2021.751999 10.3389/fgene.2021.751999]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34603401 1]. | ||
#Yau B, <i>et al.</i> (2021) "Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet." <i>iScience</i> <b>24</b>(10):103099; PMID: [https://pubmed.ncbi.nlm.nih.gov/34622154 34622154]; doi: [https://dx.doi.org/10.1016/j.isci.2021.103099 10.1016/j.isci.2021.103099]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34622154 38]. | #Yau B, <i>et al.</i> (2021) "Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet." <i>iScience</i> <b>24</b>(10):103099; PMID: [https://pubmed.ncbi.nlm.nih.gov/34622154 34622154]; doi: [https://dx.doi.org/10.1016/j.isci.2021.103099 10.1016/j.isci.2021.103099]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34622154 38]. | ||
#Di Persio S, <i>et al.</i> (2021) "Single-cell RNA-seq unravels alterations of the human spermatogonial stem cell compartment in patients with impaired spermatogenesis." <i>Cell Rep Med</i> <b>2</b>(9):100395; PMID: [https://pubmed.ncbi.nlm.nih.gov/34622232 34622232]; doi: [https://dx.doi.org/10.1016/j.xcrm.2021.100395 10.1016/j.xcrm.2021.100395]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34622232 2]. | #Di Persio S, <i>et al.</i> (2021) "Single-cell RNA-seq unravels alterations of the human spermatogonial stem cell compartment in patients with impaired spermatogenesis." <i>Cell Rep Med</i> <b>2</b>(9):100395; PMID: [https://pubmed.ncbi.nlm.nih.gov/34622232 34622232]; doi: [https://dx.doi.org/10.1016/j.xcrm.2021.100395 10.1016/j.xcrm.2021.100395]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/34622232 2]. | ||
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#Bracht T, <i>et al.</i> (2022) "Plasma Proteomics Enable Differentiation of Lung Adenocarcinoma from Chronic Obstructive Pulmonary Disease (COPD)." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36232544 36232544]; doi: [https://dx.doi.org/10.3390/ijms231911242 10.3390/ijms231911242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36232544 171]. | #Bracht T, <i>et al.</i> (2022) "Plasma Proteomics Enable Differentiation of Lung Adenocarcinoma from Chronic Obstructive Pulmonary Disease (COPD)." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36232544 36232544]; doi: [https://dx.doi.org/10.3390/ijms231911242 10.3390/ijms231911242]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36232544 171]. | ||
#Elsnicova B, <i>et al.</i> (2022) "Desmin Knock-Out Cardiomyopathy: A Heart on the Verge of Metabolic Crisis." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36233322 36233322]; doi: [https://dx.doi.org/10.3390/ijms231912020 10.3390/ijms231912020]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36233322 10]. | #Elsnicova B, <i>et al.</i> (2022) "Desmin Knock-Out Cardiomyopathy: A Heart on the Verge of Metabolic Crisis." <i>Int J Mol Sci</i> <b>23</b>(19):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36233322 36233322]; doi: [https://dx.doi.org/10.3390/ijms231912020 10.3390/ijms231912020]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36233322 10]. | ||
+ | #Pfeiffer A, <i>et al.</i> (2022) "Selective immunocapture reveals neoplastic human mast cells secrete distinct microvesicle- and exosome-like populations of KIT-containing extracellular vesicles." <i>J Extracell Vesicles</i> <b>11</b>(10):e12272; PMID: [https://pubmed.ncbi.nlm.nih.gov/36239715 36239715]; doi: [https://dx.doi.org/10.1002/jev2.12272 10.1002/jev2.12272]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36239715 4]. | ||
+ | #Speicher AM, <i>et al.</i> (2022) "Deterministic programming of human pluripotent stem cells into microglia facilitates studying their role in health and disease." <i>Proc Natl Acad Sci U S A</i> <b>119</b>(43):e2123476119; PMID: [https://pubmed.ncbi.nlm.nih.gov/36251998 36251998]; doi: [https://dx.doi.org/10.1073/pnas.2123476119 10.1073/pnas.2123476119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36251998 3]. | ||
#Kalpongnukul N, <i>et al.</i> (2022) "Phosphoproteomic Analysis Defines BABAM1 as mTORC2 Downstream Effector Promoting DNA Damage Response in Glioblastoma Cells." <i>J Proteome Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36315652 36315652]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00240 10.1021/acs.jproteome.2c00240]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36315652 400]. | #Kalpongnukul N, <i>et al.</i> (2022) "Phosphoproteomic Analysis Defines BABAM1 as mTORC2 Downstream Effector Promoting DNA Damage Response in Glioblastoma Cells." <i>J Proteome Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36315652 36315652]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00240 10.1021/acs.jproteome.2c00240]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36315652 400]. | ||
#Busso-Lopes AF, <i>et al.</i> (2022) "Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer." <i>Nat Commun</i> <b>13</b>(1):6725; PMID: [https://pubmed.ncbi.nlm.nih.gov/36344512 36344512]; doi: [https://dx.doi.org/10.1038/s41467-022-34407-1 10.1038/s41467-022-34407-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36344512 140]. | #Busso-Lopes AF, <i>et al.</i> (2022) "Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer." <i>Nat Commun</i> <b>13</b>(1):6725; PMID: [https://pubmed.ncbi.nlm.nih.gov/36344512 36344512]; doi: [https://dx.doi.org/10.1038/s41467-022-34407-1 10.1038/s41467-022-34407-1]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36344512 140]. | ||
#Jang Y, <i>et al.</i> (2022) "Mass spectrometry-based proteomics analysis of human globus pallidus from progressive supranuclear palsy patients discovers multiple disease pathways." <i>Clin Transl Med</i> <b>12</b>(11):e1076; PMID: [https://pubmed.ncbi.nlm.nih.gov/36354133 36354133]; doi: [https://dx.doi.org/10.1002/ctm2.1076 10.1002/ctm2.1076]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36354133 6]. | #Jang Y, <i>et al.</i> (2022) "Mass spectrometry-based proteomics analysis of human globus pallidus from progressive supranuclear palsy patients discovers multiple disease pathways." <i>Clin Transl Med</i> <b>12</b>(11):e1076; PMID: [https://pubmed.ncbi.nlm.nih.gov/36354133 36354133]; doi: [https://dx.doi.org/10.1002/ctm2.1076 10.1002/ctm2.1076]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36354133 6]. | ||
#Jang Y, <i>et al.</i> (2022) "Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease." <i>Mol Cell Proteomics</i> <b>22</b>(1):100452; PMID: [https://pubmed.ncbi.nlm.nih.gov/36423813 36423813]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100452 10.1016/j.mcpro.2022.100452]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36423813 5]. | #Jang Y, <i>et al.</i> (2022) "Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease." <i>Mol Cell Proteomics</i> <b>22</b>(1):100452; PMID: [https://pubmed.ncbi.nlm.nih.gov/36423813 36423813]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100452 10.1016/j.mcpro.2022.100452]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36423813 5]. | ||
+ | #Wulf M, <i>et al.</i> (2022) "The Proteome of Neuromelanin Granules in Dementia with Lewy Bodies." <i>Cells</i> <b>11</b>(22):; PMID: [https://pubmed.ncbi.nlm.nih.gov/36428966 36428966]; doi: [https://dx.doi.org/10.3390/cells11223538 10.3390/cells11223538]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36428966 49]. | ||
#Banerjee A, <i>et al.</i> (2022) "The first Pituitary Proteome Landscape from matched anterior and posterior lobes for a better understanding of the Pituitary Gland." <i>Mol Cell Proteomics</i> <b></b>:100478; PMID: [https://pubmed.ncbi.nlm.nih.gov/36470533 36470533]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100478 10.1016/j.mcpro.2022.100478]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36470533 10]. | #Banerjee A, <i>et al.</i> (2022) "The first Pituitary Proteome Landscape from matched anterior and posterior lobes for a better understanding of the Pituitary Gland." <i>Mol Cell Proteomics</i> <b></b>:100478; PMID: [https://pubmed.ncbi.nlm.nih.gov/36470533 36470533]; doi: [https://dx.doi.org/10.1016/j.mcpro.2022.100478 10.1016/j.mcpro.2022.100478]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36470533 10]. | ||
- | #Mitchell DC, <i>et al.</i> (2023) "A proteome-wide atlas of drug mechanism of action." <i>Nat Biotechnol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36593396 36593396]; doi: [https://dx.doi.org/10.1038/s41587-022-01539-0 10.1038/s41587-022-01539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36593396 | + | #Li Y, <i>et al.</i> (2023) "Proteomic analysis of radioiodine-refractory differentiated thyroid cancer identifies CHI3L1 upregulation in association with dysfunction of the sodium-iodine symporter." <i>Oncol Lett</i> <b>25</b>(1):36; PMID: [https://pubmed.ncbi.nlm.nih.gov/36589664 36589664]; doi: [https://dx.doi.org/10.3892/ol.2022.13622 10.3892/ol.2022.13622]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36589664 1]. |
+ | #Mitchell DC, <i>et al.</i> (2023) "A proteome-wide atlas of drug mechanism of action." <i>Nat Biotechnol</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36593396 36593396]; doi: [https://dx.doi.org/10.1038/s41587-022-01539-0 10.1038/s41587-022-01539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36593396 2226]. | ||
+ | #Luqman-Fatah A, <i>et al.</i> (2023) "The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction." <i>Nat Commun</i> <b>14</b>(1):203; PMID: [https://pubmed.ncbi.nlm.nih.gov/36639706 36639706]; doi: [https://dx.doi.org/10.1038/s41467-022-35757-6 10.1038/s41467-022-35757-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36639706 115]. | ||
+ | #Kreft IC, <i>et al.</i> (2023) "Proteomic landscapes of inherited platelet disorders with different etiologies." <i>J Thromb Haemost</i> <b>21</b>(2):359–372.e3; PMID: [https://pubmed.ncbi.nlm.nih.gov/36700500 36700500]; doi: [https://dx.doi.org/10.1016/j.jtha.2022.11.021 10.1016/j.jtha.2022.11.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36700500 119]. | ||
+ | #Weiβ M, <i>et al.</i> (2023) "Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control." <i>Cell Rep</i> <b>42</b>(2):112045; PMID: [https://pubmed.ncbi.nlm.nih.gov/36701236 36701236]; doi: [https://dx.doi.org/10.1016/j.celrep.2023.112045 10.1016/j.celrep.2023.112045]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36701236 45]. | ||
+ | #Li C, <i>et al.</i> (2023) "SUMO Proteomics Analyses Identify Protein Inhibitor of Activated STAT-Mediated Regulatory Networks Involved in Cell Cycle and Cell Proliferation." <i>J Proteome Res</i>; PMID: [https://pubmed.ncbi.nlm.nih.gov/36723483 36723483]; doi: [https://dx.doi.org/10.1021/acs.jproteome.2c00557 10.1021/acs.jproteome.2c00557]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36723483 114]. | ||
+ | #van Tienderen GS, <i>et al.</i> (2023) "Tumor decellularization reveals proteomic and mechanical characteristics of the extracellular matrix of primary liver cancer." <i>Biomater Adv</i> <b>146</b>:213289; PMID: [https://pubmed.ncbi.nlm.nih.gov/36724550 36724550]; doi: [https://dx.doi.org/10.1016/j.bioadv.2023.213289 10.1016/j.bioadv.2023.213289]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36724550 54]. | ||
+ | #Militaru IV, <i>et al.</i> (2022) "New panel of biomarkers to discriminate between amelanotic and melanotic metastatic melanoma." <i>Front Oncol</i> <b>12</b>:1061832; PMID: [https://pubmed.ncbi.nlm.nih.gov/36776379 36776379]; doi: [https://dx.doi.org/10.3389/fonc.2022.1061832 10.3389/fonc.2022.1061832]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36776379 81]. | ||
+ | #Akter F, <i>et al.</i> (2023) "Multi Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins." <i>Mol Cell Proteomics</i> <b></b>:100509; PMID: [https://pubmed.ncbi.nlm.nih.gov/36791992 36791992]; doi: [https://dx.doi.org/10.1016/j.mcpro.2023.100509 10.1016/j.mcpro.2023.100509]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36791992 30]. | ||
+ | #Otčenášková T, <i>et al.</i> (2023) "Proteomic analysis of the mouse sperm acrosome - towards an understanding of an organelle with diverse functionality." <i>Eur J Cell Biol</i> <b>102</b>(2):151296; PMID: [https://pubmed.ncbi.nlm.nih.gov/36805822 36805822]; doi: [https://dx.doi.org/10.1016/j.ejcb.2023.151296 10.1016/j.ejcb.2023.151296]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/36805822 20]. | ||
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GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION:Many datasets/papers contain serious errors in their metadata/methods sections. When using data from repositories, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methods, etc.) that may impact on your use of the data. We have corrected for as many of these errors as we could detect, but there is no way to be sure that we found them all. When attempting to analyze or reproduce results, keep in mind the likelihood that key parts of the experimental methods may have been recorded incorrectly in the associated metadata or manuscript.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of April 9, 2023.