Experiment ID Name Citation Description URL PMID Current 1536 [Default Assignments] Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules "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." "Phosphotyrosine analysis of HMEC cells in response to EGF, measured at 0, 5, 10 and 30minutes." 15951569 1 1412 [Miscleavages removed] [Default Assignments] Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks "Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM. Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5." Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. -- Removed the miscleaved forms of redundant phosphopeptides. 17389395 1 1546 Akt-RSK-S6 kinase signaling networks activated by oncogenic receptor tyrosine kinases "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." "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." 20736484 1 1803 "UniprotKB MOD_RES Dec. 16, 2016" SIB Swiss Institute of Bioinformatics Members. Nucleic acids research. 2016-January. Vol 44. D27-37. "UniProtKB MOD_RES for all eukaryotes as of December 16, 2016" http://www.uniprot.org/ 0 1432 "[MG-132 treatment set] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles" "Wagner SA,Beli P,Weinert BT,Nielsen ML,Cox J,Mann M,Choudhary C. Molecular & cellular proteomics : MCP. 2011-October. Vol 10. 1-13." 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). 21890473 1 1682 Tyrosine Phosphorylation of the Lyn Src Homology 2 (SH2) Domain Modulates Its Binding Affinity and Specificity "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." "The SH2 domain of Lyn, and the phosphorylated form of Lyn (created by Epha4 kinase) were used to bait phosphopeptides from cancer cell lines." 25587033 1 1431 "A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles" "Wagner SA,Beli P,Weinert BT,Nielsen ML,Cox J,Mann M,Choudhary C. Molecular & cellular proteomics : MCP. 2011-October. Vol 10. 1-13." Identification of ubiquitylation sites in HEK-293T and MV-411 cells using di-Gly-lysine specific antibody enrichment and mass spectrometry 21890473 1 1688 UniProtKB CARBOHYD The UniProt Consortium. Nucleic Acids Research. 2015-January. Vol 43. 204-12. "CARBOHYD annotations from human proteins downloaded November 17, 2015" http://www.uniprot.org/ 0 1599 [Default Assignments] Effects of HER2 overexpression on cell signaling networks governing proliferation and migration "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." Quantitative phosphotyrosine analysis of wild type and HER2 overexpressing human mammary epithelial cells stimulated by EGF and HRG. 17016520 1 1564 Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants "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." HEK293 cells expressing DDR2 were stimulated with soluble collagen I and phosphorylation was quantitatively profiled across time. 23822953 1 1565 An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells "Joughin BA,Naegle KM,Huang PH,Yaffe MB,Lauffenburger DA,White FM. Molecular bioSystems. 2008-December. Vol 5. 59-67." "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." 19081932 1 1825 The Induction of Serine/Threonine Protein Phosphorylations by a PDGFR/TrkA Chimera in Stably Transfected PC12 Cells "Biarc J,Chalkley RJ,Burlingame AL,Bradshaw RA. Molecular & cellular proteomics : MCP. 2012-May. Vol 11. 15-30." 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. 22027198 1 1826 Dissecting the roles of tyrosines 490 and 785 of TrkA protein in the induction of downstream protein phosphorylation using chimeric receptors "Biarc J,Chalkley RJ,Burlingame AL,Bradshaw RA. The Journal of biological chemistry. 2013-June. Vol 288. 16606-18." "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." 23589303 1 1575 dbPTM 3.0 experimentally verified PTM sites "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." dbPTM 3.0 downloaded 09/25/2014. Experimentally verified PTM table. http://dbptm.mbc.nctu.edu.tw/ 23193290 1 1704 [Samples with poor pre-treatment normalization removed] MEK-Dependent Negative Feedback Underlies BCR-ABL-Mediated Oncogene Addiction "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." "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." 24362263 1 1323 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." Release of Phospho.ELM v9.0 http://phospho.elm.eu.org/ 21062810 1 1715 Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML "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." "Quantitative measurement of phosphorylation in a BCR-ABLT315I mouse model. Treatment includes control and addition of tyrosine kinase inhibitors (bosutinib, danusertib, and the combination)" 23023260 1 1718 Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels "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." 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. 24719451 1 1719 [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 "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." 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. 24719451 1 1723 Proteogenomics connects somatic mutations to signalling in breast cancer "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." Phosphoproteomics of 77 breast cancer patient samples from the TCGA. 27251275 1 1343 A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T Cell Receptor Activation "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." Phosphoproteomic analysis of T-cell receptor signaling in Zap-70 null cells vs. reconstructed Zap-70 cells 19605366 1 1344 O-GlycBase v6.00 "Gupta R,Birch H,Rapacki K,Brunak S,Hansen JE. Nucleic acids research. 1999-March. Vol 27. 370-2." Database of O-glycosylated and C-glycosylated proteins showing experimentally verified sites only. http://www.cbs.dtu.dk/databases/OGLYCBASE/ 9847232 1 1345 Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium "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." "Understanding cross-talk between phosphorylation and lysine acetylation in wild type vs. mutants Mycoplasma pneumoniae (lacking PknB, HPrk, or PrpC)" 22373819 1 1617 Mass spectrometry-based quantification of the cellular response to methyl methanesulfonate treatment in human cells. "Aslanian A,Yates JR III,Hunter T. DNA repair. 2014-February. Vol 15. 29-38." Methyl methanesulfonate (MMS) was used to induce DNA damage in HeLa cells. SILAC-based quantitative proteomics was used to measure changes in phosphorylation. 24461736 1 1618 MEK-Dependent Negative Feedback Underlies BCR-ABL-Mediated Oncogene Addiction "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." "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." 24362263 1 1367 Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks "Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM. Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5." Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. 17389395 1 1369 Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer "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." Characterized tyrosine kinase signaling of 41 lung cancer cell lines using a phosphoproteomic approach. http://www.sciencedirect.com/science/article/pii/S009286740701522X 18083107 1 1885 Phosphorylation site dynamics of early T-cell receptor signaling "Chylek LA,Akimov V,Dengjel J,Rigbolt KT,Hu B,Hlavacek WS,Blagoev B. PloS one. 2014-August. Vol 9. e104240." "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." 25147952 1 1381 [Default Assignments] Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks "Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM. Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5." Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. 17389395 1 1777 Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder "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." "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." 27642862 1 1386 [Miscleavages Removed][Default Assignments] Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks "Wolf-Yadlin A,Hautaniemi S,Lauffenburger DA,White FM. Proceedings of the National Academy of Scienc. 2007-April. Vol 104. 5860-5." "Phosphotyrosine dynamics of EGF-stimulated human mammary epithelial cells. When multiple peptide fragments representing the same phosphorylation site existed, the miscleaved peptide was removed." 17389395 1 1387 Effects of HER2 overexpression on cell signaling networks governing proliferation and migration "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." Quantitative phosphotyrosine analysis of wild type and HER2 overexpressing human mammary epithelial cells stimulated by EGF and HRG. 17016520 1 1388 Lysine acetylation targets protein complexes and co-regulates major cellular functions "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." 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 19608861 1 1390 System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation "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." SILAC-based profiling of phosphopeptides from human embryonic stem cells. PMA and NCM stimulation in time relative to unstimulated. 21406692 1 1391 Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species "Beltrao P,Trinidad JC,Fiedler D,Roguev A,Lim WA,Shokat KM,Burlingame AL,Krogan NJ. PLoS biology. 2009-June. Vol 7. e1000134." "Yeast phosphoproteome profiling of A. albicans, S. pombe, and S. cerevisiae" 19547744 1 1521 Signaling networks assembled by oncogenic EGFR and c-MET: Profiling of lung cancer cell lines "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." "Supplementary Table 4, tyrosine phosphorylation profiling of seven lung cancer cell lines. Quantitative data represents number of times phosphopeptide was identified in PhosphoScan experiment." 18180459 1 1395 HPRD: Human Protein Reference Database Curated Modifications "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." July 2010 download of HPRD's modification table. http://hprd.org/ 18988627 1 1402 Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules "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." "Phosphotyrosine analysis of HMEC cells in response to EGF, measured at 0, 5, 10 and 30minutes." 15951569 1 1787 "[Cell lines specified] Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer, with cell lines specified" "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." 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. 18083107 1 1790 PhosphositePlus November 2016 "Hornbeck PV,Zhang B,Murray B,Kornhauser JM,Latham V,Skrzypek E. Nucleic acids research. 2015-January. Vol 43. D512-20." Phosphorylation; Methylation; Acetylation; Ubiquitination; Sumoylation; O-GlcNAc http://www.phosphosite.org/homeAction.action 25514926 0 1886 UniProt Human Proteome Integration 2026-01-06 UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489. doi: 10.1093/nar/gkaa1100. PMID: 33237286; PMCID: PMC7779014. Integration of UniProt Human proteome data into ProteomeScout. This dataset includes protein sequences and post-translational modifications (PTMs) curated by UniProt. https://www.uniprot.org/ 33237286 1 1887 PhosphoSitePlus Proteome Integration 2026-01-07 PhosphoSitePlus Consortium. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2014 Jan;42(Database issue):D431-7. doi: 10.1093/nar/gkt1249. PMID: 24234440; PMCID: PMC3965117. Integration of PhosphoSitePlus proteome data into ProteomeScout. This dataset includes protein sequences and post-translational modifications (PTMs) curated by PhosphoSitePlus. https://www.phosphosite.org/ 24234440 1