Compendia
| Compendia | Description | Authors | Journal Info |
|---|---|---|---|
| HPRD: Human Protein Reference Database Curated Modifications | July 2010 download of HPRD's modification table. | Keshava Prasad TS,Goel R,Kandasamy K,Keerthikumar S,Kumar S,Mathivanan S,Telikicherla D,Raju R,Shafreen B,Venugopal A,Balakrishnan L,Marimuthu A,Banerjee S,Somanathan DS,Sebastian A,Rani S,Ray S,Harrys Kishore CJ,Kanth S,Ahmed M,Kashyap MK,Mohmood R,Ramachandra YL,Krishna V,Rahiman BA,Mohan S,Ranganathan P,Ramabadran S,Chaerkady R,Pandey A | Nucleic acids research. 2008-December. Vol 37. D767-72. |
| O-GlycBase v6.00 | Database of O-glycosylated and C-glycosylated proteins showing experimentally verified sites only. | Gupta R,Birch H,Rapacki K,Brunak S,Hansen JE | Nucleic acids research. 1999-March. Vol 27. 370-2. |
| Phospho.ELM v9.0 | Release of Phospho.ELM v9.0 | Dinkel H,Chica C,Via A,Gould CM,Jensen LJ,Gibson TJ,Diella F | Nucleic acids research. 2010-December. Vol 39. D261-7. |
| PhosphositePlus November 2016 | Phosphorylation; Methylation; Acetylation; Ubiquitination; Sumoylation; O-GlcNAc | Hornbeck PV,Zhang B,Murray B,Kornhauser JM,Latham V,Skrzypek E | Nucleic acids research. 2015-January. Vol 43. D512-20. |
| UniProtKB CARBOHYD | CARBOHYD annotations from human proteins downloaded November 17, 2015 | The UniProt Consortium | Nucleic Acids Research. 2015-January. Vol 43. 204-12. |
| UniprotKB MOD_RES Dec. 16, 2016 | UniProtKB MOD_RES for all eukaryotes as of December 16, 2016 | SIB Swiss Institute of Bioinformatics Members | Nucleic acids research. 2016-January. Vol 44. D27-37. |
| dbPTM 3.0 experimentally verified PTM sites | dbPTM 3.0 downloaded 09/25/2014. Experimentally verified PTM table. | Lu CT,Huang KY,Su MG,Lee TY,Bretana NA,Chang WC,Chen YJ,Chen YJ,Huang HD | Nucleic acids research. 2012-December. Vol 41. D295-305. |
Experiments
| Experiment | Description | Authors | Journal Info |
|---|---|---|---|
| A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T Cell Receptor Activation | Phosphoproteomic analysis of T-cell receptor signaling in Zap-70 null cells vs. reconstructed Zap-70 cells | Nguyen V,Cao L,Lin JT,Hung N,Ritz A,Yu K,Jianu R,Ulin SP,Raphael BJ,Laidlaw DH,Brossay L,Salomon AR | Molecular & cellular proteomics : MCP. 2009-December. Vol 8. 2418-31. |
| A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles | Identification of ubiquitylation sites in HEK-293T and MV-411 cells using di-Gly-lysine specific antibody enrichment and mass spectrometry | Wagner SA,Beli P,Weinert BT,Nielsen ML,Cox J,Mann M,Choudhary C | Molecular & cellular proteomics : MCP. 2011-October. Vol 10. 1-13. |
| [MG-132 treatment set] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles | Identification of ubiquitylation sites in HEK-293T and MV-411 cells using di-Gly-lysine specific antibody enrichment and mass spectrometry -- The quantitative measurements (SILAC) of ubiquitylation in response to MG-132 treatment (proteosome inhibition for 4 hours compared to DMSO control). | Wagner SA,Beli P,Weinert BT,Nielsen ML,Cox J,Mann M,Choudhary C | Molecular & cellular proteomics : MCP. 2011-October. Vol 10. 1-13. |
| Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases | Antibody-based enrichment of Akt, RSK, and S6 kinase substrates and subsequent monitoring of quantitative phosphorylation changes in cells treated with pathway inhibitors (SILAC). Data indicates ratio of L/H SILAC labels where H (heavy) is DMSO control. The run describes which condition was used. | Moritz A,Li Y,Guo A,Villen J,Wang Y,MacNeill J,Kornhauser J,Sprott K,Zhou J,Possemato A,Ren JM,Hornbeck P,Cantley LC,Gygi SP,Rush J,Comb MJ | Science signaling. 2010-August. Vol 3. ra64. |
| An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells | U87 cell lines expressing the EGFRVIII (truncation of EGFR) at various levels (Medium, High, and SuperHigh) and a kinase dead version of the receptor were measured, quantitatively, for phosphorylation levels. | Joughin BA,Naegle KM,Huang PH,Yaffe MB,Lauffenburger DA,White FM | Molecular bioSystems. 2008-December. Vol 5. 59-67. |
| Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium | Understanding cross-talk between phosphorylation and lysine acetylation in wild type vs. mutants Mycoplasma pneumoniae (lacking PknB, HPrk, or PrpC) | van Noort V,Seebacher J,Bader S,Mohammed S,Vonkova I,Betts MJ,Kuhner S,Kumar R,Maier T,O'Flaherty M,Rybin V,Schmeisky A,Yus E,Stulke J,Serrano L,Russell RB,Heck AJ,Bork P,Gavin AC | Molecular systems biology. 2012-February. Vol 8. 571. |
| Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors | A PDGFR (extracellular region) was fused to the rat TRKA transmembrane and intracellular region to create a receptor tyrosine chimera with TRKA-competent signaling that is responsive to PDGF. Then intracellular tyrosine positions, Y490 and Y785 were mutated to isolate the signaling roles of each. Phosphoproteomic measurements were done using SILAC and LC-MS/MS. | Biarc J,Chalkley RJ,Burlingame AL,Bradshaw RA | The Journal of biological chemistry. 2013-June. Vol 288. 16606-18. |
| Effects of HER2 overexpression on cell signaling networks governing proliferation and migration | Quantitative phosphotyrosine analysis of wild type and HER2 overexpressing human mammary epithelial cells stimulated by EGF and HRG. | Wolf-Yadlin A,Kumar N,Zhang Y,Hautaniemi S,Zaman M,Kim HD,Grantcharova V,Lauffenburger DA,White FM | Molecular systems biology. 2006-October. Vol 2. 54. |
| [Default Assignments] Effects of HER2 overexpression on cell signaling networks governing proliferation and migration | Quantitative phosphotyrosine analysis of wild type and HER2 overexpressing human mammary epithelial cells stimulated by EGF and HRG. | Wolf-Yadlin A,Kumar N,Zhang Y,Hautaniemi S,Zaman M,Kim HD,Grantcharova V,Lauffenburger DA,White FM | Molecular systems biology. 2006-October. Vol 2. 54. |
| Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species | Yeast phosphoproteome profiling of A. albicans, S. pombe, and S. cerevisiae | Beltrao P,Trinidad JC,Fiedler D,Roguev A,Lim WA,Shokat KM,Burlingame AL,Krogan NJ | PLoS biology. 2009-June. Vol 7. e1000134. |
| Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer | Characterized tyrosine kinase signaling of 41 lung cancer cell lines using a phosphoproteomic approach. | Rikova K,Guo A,Zeng Q,Possemato A,Yu J,Haack H,Nardone J,Lee K,Reeves C,Li Y,Hu Y,Tan Z,Stokes M,Sullivan L,Mitchell J,Wetzel R,Macneill J,Ren JM,Yuan J,Bakalarski CE,Villen J,Kornhauser JM,Smith B,Li D,Zhou X,Gygi SP,Gu TL,Polakiewicz RD,Rush J,Comb MJ | Cell. 2007-December. Vol 131. 1190-203. |
| Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels | Ovarian and breast human tumors were collected and placed under ischemic conditions. The classification of a phosphoprotein responsive to ischemia is set to TRUE (or 1) if a change was detected in one of the samples as a result of ischemia. | Mertins P,Yang F,Liu T,Mani DR,Petyuk VA,Gillette MA,Clauser KR,Qiao JW,Gritsenko MA,Moore RJ,Levine DA,Townsend R,Erdmann-Gilmore P,Snider JE,Davies SR,Ruggles KV,Fenyo D,Kitchens RT,Li S,Olvera N,Dao F,Rodriguez H,Chan DW,Liebler D,White F,Rodland KD,Mills GB,Smith RD,Paulovich AG,Ellis M,Carr SA | Molecular & cellular proteomics : MCP. 2014-July. Vol 13. 1690-704. |
| [Only sites that respond to ischemia] Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels | Ovarian and breast human tumors were collected and placed under ischemic conditions. The classification of a phosphoprotein responsive to ischemia is set to TRUE (or 1) if a change was detected in one of the samples as a result of ischemia. -- This is a subset of the parent dataset for only those phosphorylation sites that were considered to respond to ischemia. | Mertins P,Yang F,Liu T,Mani DR,Petyuk VA,Gillette MA,Clauser KR,Qiao JW,Gritsenko MA,Moore RJ,Levine DA,Townsend R,Erdmann-Gilmore P,Snider JE,Davies SR,Ruggles KV,Fenyo D,Kitchens RT,Li S,Olvera N,Dao F,Rodriguez H,Chan DW,Liebler D,White F,Rodland KD,Mills GB,Smith RD,Paulovich AG,Ellis M,Carr SA | Molecular & cellular proteomics : MCP. 2014-July. Vol 13. 1690-704. |
| Lysine acetylation targets protein complexes and co-regulates major cellular functions | MS discovery of acetylation in MV4-11 (myeloid leukemia cell line) cells. Acetyl-lysine antibody pull down plus isoelectric focusing. Addition of KDAC inhibitors SAHA and MS-275 experiment also included | Choudhary C,Kumar C,Gnad F,Nielsen ML,Rehman M,Walther TC,Olsen JV,Mann M | Science (New York, N.Y.). 2009-August. Vol 325. 834-40. |
| MEK-Dependent Negative Feedback Underlies BCR-ABL-Mediated Oncogene Addiction | Quantitative measurements of phosphotyrosine dynamics in K562 cells (patient-derived CML cell line) treated with a high dose of dasatinib (100nmol/L). Measurements taking before treatment, at washout (EOE), and 3 and 6 hours post-treatment. | Asmussen J,Lasater EA,Tajon C,Oses-Prieto J,Jun YW,Taylor BS,Burlingame A,Craik CS,Shah NP | Cancer discovery. 2014-February. Vol 4. 200-15. |
| Mass spectrometry-based quantification of the cellular response to methyl methanesulfonate treatment in human cells. | Methyl methanesulfonate (MMS) was used to induce DNA damage in HeLa cells. SILAC-based quantitative proteomics was used to measure changes in phosphorylation. | Aslanian A,Yates JR III,Hunter T | DNA repair. 2014-February. Vol 15. 29-38. |
| Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks | Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. | Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM | Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5. |
| [Default Assignments] Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks | Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. | Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM | Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5. |
| [Miscleavages Removed][Default Assignments] Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks | Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. When multiple peptide fragments representing the same phosphorylation site existed, the miscleaved peptide was removed. | Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM | Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5. |
| [Miscleavages removed] [Default Assignments] Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks | Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. -- Removed the miscleaved forms of redundant phosphopeptides. | Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM | Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5. |
| Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants | HEK293 cells expressing DDR2 were stimulated with soluble collagen I and phosphorylation was quantitatively profiled across time. | Iwai LK,Payne LS,Luczynski MT,Chang F,Xu H,Clinton RW,Paul A,Esposito EA,Gridley S,Leitinger B,Naegle KM,Huang PH | The Biochemical journal. 2013-August. Vol 454. 501-13. |
| Phosphorylation site dynamics of early T-cell receptor signaling | Early T-cell signaling, activated by anti-CD28 antibody, measured at 0, 5, 15, 30, and 60 seconds. Phosphotyrosine enrichment and LC-MS/MS with SILAC labels. Quantification is the log2 of the stimulated to unstimulated sample. | Chylek LA,Akimov V,Dengjel J,Rigbolt KT,Hu B,Hlavacek WS,Blagoev B | PloS one. 2014-August. Vol 9. e104240. |
| Proteogenomics connects somatic mutations to signalling in breast cancer | Phosphoproteomics of 77 breast cancer patient samples from the TCGA. | Mertins P,Mani DR,Ruggles KV,Gillette MA,Clauser KR,Wang P,Wang X,Qiao JW,Cao S,Petralia F,Kawaler E,Mundt F,Krug K,Tu Z,Lei JT,Gatza ML,Wilkerson M,Perou CM,Yellapantula V,Huang KL,Lin C,McLellan MD,Yan P,Davies SR,Townsend RR,Skates SJ,Wang J,Zhang B,Kinsinger CR,Mesri M,Rodriguez H,Ding L,Paulovich AG,Fenyo D,Ellis MJ,Carr SA | Nature. 2016-June. Vol 534. 55-62. |
| Signaling networks assembled by oncogenic EGFR and c-MET: Profiling of lung cancer cell lines | Supplementary Table 4, tyrosine phosphorylation profiling of seven lung cancer cell lines. Quantitative data represents number of times phosphopeptide was identified in PhosphoScan experiment. | Guo A,Villen J,Kornhauser J,Lee KA,Stokes MP,Rikova K,Possemato A,Nardone J,Innocenti G,Wetzel R,Wang Y,MacNeill J,Mitchell J,Gygi SP,Rush J,Polakiewicz RD,Comb MJ | Proceedings of the National Academy of Scienc. 2008-January. Vol 105. 692-7. |
| System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation | SILAC-based profiling of phosphopeptides from human embryonic stem cells. PMA and NCM stimulation in time relative to unstimulated. | Rigbolt KT,Prokhorova TA,Akimov V,Henningsen J,Johansen PT,Kratchmarova I,Kassem M,Mann M,Olsen JV,Blagoev B | Science signaling. 2011-March. Vol 4. rs3. |
| Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML | Quantitative measurement of phosphorylation in a BCR-ABLT315I mouse model. Treatment includes control and addition of tyrosine kinase inhibitors (bosutinib, danusertib, and the combination) | Winter GE,Rix U,Carlson SM,Gleixner KV,Grebien F,Gridling M,Muller AC,Breitwieser FP,Bilban M,Colinge J,Valent P,Bennett KL,White FM,Superti-Furga G | Nature chemical biology. 2012-October. Vol 8. 905-12. |
| The Induction of Serine/Threonine Protein Phosphorylations by a PDGFR/TrkA Chimera in Stably Transfected PC12 Cells | A PDGFR (extracellular region) was fused to the rat TRKA transmembrane and intracellular region to create a receptor tyrosine chimera with TRKA-competent signaling that is responsive to PDGF. Phosphoproteomic measurements were done using SILAC and LC-MS/MS. | Biarc J,Chalkley RJ,Burlingame AL,Bradshaw RA | Molecular & cellular proteomics : MCP. 2012-May. Vol 11. 15-30. |
| Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules | Phosphotyrosine analysis of HMEC cells in response to EGF, measured at 0, 5, 10 and 30minutes. | Zhang Y,Wolf-Yadlin A,Ross PL,Pappin DJ,Rush J,Lauffenburger DA,White FM | Molecular & cellular proteomics : MCP. 2005-September. Vol 4. 1240-50. |
| [Default Assignments] Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules | Phosphotyrosine analysis of HMEC cells in response to EGF, measured at 0, 5, 10 and 30minutes. | Zhang Y,Wolf-Yadlin A,Ross PL,Pappin DJ,Rush J,Lauffenburger DA,White FM | Molecular & cellular proteomics : MCP. 2005-September. Vol 4. 1240-50. |
| Tyrosine Phosphorylation of the Lyn Src Homology 2 (SH2) Domain Modulates Its Binding Affinity and Specificity | The SH2 domain of Lyn, and the phosphorylated form of Lyn (created by Epha4 kinase) were used to bait phosphopeptides from cancer cell lines. | Jin LL,Wybenga-Groot LE,Tong J,Taylor P,Minden MD,Trudel S,McGlade CJ,Moran MF | Molecular & cellular proteomics : MCP. 2015-March. Vol 14. 695-706. |
| Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder | A SRC SH2 domain superbinder was used to enrich for tyrosine phosphorylation from nine human cell lines (HeLa, Jurkat, Bel7402, Hep-G2, MCF-7, BT-474, SK-BR-3, MDA-MB-231, MCF-10A) treated with pervanadate. | Bian Y,Li L,Dong M,Liu X,Kaneko T,Cheng K,Liu H,Voss C,Cao X,Wang Y,Litchfield D,Ye M,Li SS,Zou H | Nature chemical biology. 2016-September. Vol 12. 959-66. |
| [Cell lines specified] Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer, with cell lines specified | Characterized tyrosine kinase signaling of 41 lung cancer cell lines using a phosphoproteomic approach. This experiment contains the cell line or sample used as a run type. | Rikova K,Guo A,Zeng Q,Possemato A,Yu J,Haack H,Nardone J,Lee K,Reeves C,Li Y,Hu Y,Tan Z,Stokes M,Sullivan L,Mitchell J,Wetzel R,Macneill J,Ren JM,Yuan J,Bakalarski CE,Villen J,Kornhauser JM,Smith B,Li D,Zhou X,Gygi SP,Gu TL,Polakiewicz RD,Rush J,Comb MJ | Cell. 2007-December. Vol 131. 1190-203. |
| [Samples with poor pre-treatment normalization removed] MEK-Dependent Negative Feedback Underlies BCR-ABL-Mediated Oncogene Addiction | Quantitative measurements of phosphotyrosine dynamics in K562 cells (patient-derived CML cell line) treated with a high dose of dasatinib (100nmol/L). Measurements taking before treatment, at washout (EOE), and 3 and 6 hours post-treatment (all treatments were for 20minutes). -- Those samples that had issues with the pre-treatment normalizations were removed in this extension. | Asmussen J,Lasater EA,Tajon C,Oses-Prieto J,Jun YW,Taylor BS,Burlingame A,Craik CS,Shah NP | Cancer discovery. 2014-February. Vol 4. 200-15. |