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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 January 1, 2020. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (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: [http://www.ncbi.nlm.nih.gov/pubmed/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, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (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: [http://www.ncbi.nlm.nih.gov/pubmed/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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#Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29139296 60]. | #Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29139296 60]. | ||
#Worzfeld T, Finkernagel F, Reinartz S, Konzer A, Adhikary T, Nist A, Stiewe T, Wagner U, Looso M, Graumann J, Müller R, (2017) "Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29141914 29141914]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000400 10.1074/mcp.RA117.000400]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29141914 121]. | #Worzfeld T, Finkernagel F, Reinartz S, Konzer A, Adhikary T, Nist A, Stiewe T, Wagner U, Looso M, Graumann J, Müller R, (2017) "Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29141914 29141914]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000400 10.1074/mcp.RA117.000400]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29141914 121]. | ||
+ | #Raffel S, Falcone M, Kneisel N, Hansson J, Wang W, Lutz C, Bullinger L, Poschet G, Nonnenmacher Y, Barnert A, Bahr C, Zeisberger P, Przybylla A, Sohn M, Tönjes M, Erez A, Adler L, Jensen P, Scholl C, Fröhling S, Cocciardi S, Wuchter P, Thiede C, Flörcken A, Westermann J, Ehninger G, Lichter P, Hiller K, Hell R, Herrmann C, Ho AD, Krijgsveld J, Radlwimmer B, Trumpp A, (2017) "BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation." <i>Nature</i> <b>551</b>(7680):384–388; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29144447 29144447]; doi: [https://dx.doi.org/10.1038/nature24294 10.1038/nature24294]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29144447 10]. | ||
#Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145436 57]. | #Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145436 57]. | ||
#Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145658 4]. | #Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145658 4]. | ||
Line 2,063: | Line 2,064: | ||
#Dybas JM, O'Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM, (2019) "Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4<sup>+</sup> T cells." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31061531 31061531]; doi: [https://dx.doi.org/10.1038/s41590-019-0381-6 10.1038/s41590-019-0381-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31061531 118]. | #Dybas JM, O'Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM, (2019) "Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4<sup>+</sup> T cells." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31061531 31061531]; doi: [https://dx.doi.org/10.1038/s41590-019-0381-6 10.1038/s41590-019-0381-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31061531 118]. | ||
#Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P, (2019) "Proteomic analysis of meningiomas reveals clinically-distinct molecular patterns." <i>Neuro Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31077268 31077268]; doi: [https://dx.doi.org/10.1093/neuonc/noz084 10.1093/neuonc/noz084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31077268 78]. | #Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P, (2019) "Proteomic analysis of meningiomas reveals clinically-distinct molecular patterns." <i>Neuro Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31077268 31077268]; doi: [https://dx.doi.org/10.1093/neuonc/noz084 10.1093/neuonc/noz084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31077268 78]. | ||
+ | #Spörrer M, Prochnicki A, Tölle RC, Nyström A, Esser PR, Homberg M, Athanasiou I, Zingkou E, Schilling A, Gerum R, Thievessen I, Winter L, Bruckner-Tuderman L, Fabry B, Magin TM, Dengjel J, Schröder R, Kiritsi D, (2019) "Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders." <i>EBioMedicine</i> <b>44</b>:502–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078522 31078522]; doi: [https://dx.doi.org/10.1016/j.ebiom.2019.04.062 10.1016/j.ebiom.2019.04.062]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078522 41]. | ||
#Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | #Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | ||
#Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | #Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | ||
#Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T, (2019) "Proteomic and Metabolomic Profiling of <i>Deinococcus radiodurans</i> Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions." <i>Front Microbiol</i> <b>10</b>:909; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31110498 31110498]; doi: [https://dx.doi.org/10.3389/fmicb.2019.00909 10.3389/fmicb.2019.00909]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31110498 17]. | #Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T, (2019) "Proteomic and Metabolomic Profiling of <i>Deinococcus radiodurans</i> Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions." <i>Front Microbiol</i> <b>10</b>:909; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31110498 31110498]; doi: [https://dx.doi.org/10.3389/fmicb.2019.00909 10.3389/fmicb.2019.00909]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31110498 17]. | ||
#Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | #Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | ||
- | #Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ, (2019) "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS<sup>G13D</sup> mutation." <i>Br J Cancer</i> <b>121</b>(1):37–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31133691 31133691]; doi: [https://dx.doi.org/10.1038/s41416-019-0477-7 10.1038/s41416-019-0477-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31133691 | + | #Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ, (2019) "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS<sup>G13D</sup> mutation." <i>Br J Cancer</i> <b>121</b>(1):37–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31133691 31133691]; doi: [https://dx.doi.org/10.1038/s41416-019-0477-7 10.1038/s41416-019-0477-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31133691 523]. |
#Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | #Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | ||
#Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | #Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | ||
Line 2,124: | Line 2,126: | ||
#Kenny A, Jiménez-Mateos EM, Zea-Sevilla MA, Rábano A, Gili-Manzanaro P, Prehn JHM, Henshall DC, Ávila J, Engel T, Hernández F, (2019) "Proteins and microRNAs are differentially expressed in tear fluid from patients with Alzheimer's disease." <i>Sci Rep</i> <b>9</b>(1):15437; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31659197 31659197]; doi: [https://dx.doi.org/10.1038/s41598-019-51837-y 10.1038/s41598-019-51837-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31659197 32]. | #Kenny A, Jiménez-Mateos EM, Zea-Sevilla MA, Rábano A, Gili-Manzanaro P, Prehn JHM, Henshall DC, Ávila J, Engel T, Hernández F, (2019) "Proteins and microRNAs are differentially expressed in tear fluid from patients with Alzheimer's disease." <i>Sci Rep</i> <b>9</b>(1):15437; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31659197 31659197]; doi: [https://dx.doi.org/10.1038/s41598-019-51837-y 10.1038/s41598-019-51837-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31659197 32]. | ||
#Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | #Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | ||
- | #Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 | + | #Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 193]. |
+ | #Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM, (2019) "Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity." <i>Genes Dev</i> <b>33</b>(23-24):1751–1774; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31753913 31753913]; doi: [https://dx.doi.org/10.1101/gad.331231.119 10.1101/gad.331231.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31753913 66]. | ||
+ | #Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y, (2019) "Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31773964 31773964]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00590 10.1021/acs.jproteome.9b00590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31773964 16]. | ||
+ | #Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D, (2019) "Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31848261 31848261]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001641 10.1074/mcp.TIR119.001641]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31848261 208]. |
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 papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
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 January 1, 2020.