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--- |
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size_categories: |
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- 1M<n<10M |
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pretty_name: CF/MS Homo sapiens Elution Profile PPI Dataset |
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tags: |
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- biology |
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- chemistry |
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dataset_summary: >- |
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Processed data from several *Homo sapiens* protein co-fractionation mass |
|
spectrometry (CF/MS) experiments, as well as positive/negative protein-protein |
|
interaction (PPI) labels for each pair. Collated, maintained by the Drew Lab at |
|
University of Illinois at Chicago. |
|
citation_bibtex: |
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- >- |
|
@article{Connelly2018, title = {Analysis of Human Nuclear Protein Complexes by |
|
Quantitative Mass Spectrometry Profiling}, volume = {18}, ISSN = {1615-9861}, |
|
url = {http://dx.doi.org/10.1002/pmic.201700427}, DOI = |
|
{10.1002/pmic.201700427}, number = {11}, journal = {PROTEOMICS}, publisher = |
|
{Wiley}, author = {Connelly, Katelyn E. and Hedrick, Victoria and Paschoal |
|
Sobreira, Tiago Jose and Dykhuizen, Emily C. and Aryal, Uma K.}, year = |
|
{2018}, month = may} |
|
- >- |
|
@article{Kirkwood2013, title = {Characterization of Native Protein Complexes |
|
and Protein Isoform Variation Using Size-fractionation-based Quantitative |
|
Proteomics}, volume = {12}, ISSN = {1535-9476}, url = |
|
{http://dx.doi.org/10.1074/mcp.M113.032367}, DOI = {10.1074/mcp.m113.032367}, |
|
number = {12}, journal = {Molecular & Cellular Proteomics}, publisher = |
|
{Elsevier BV}, author = {Kirkwood, Kathryn J. and Ahmad, Yasmeen and |
|
Larance, Mark and Lamond, Angus I.}, year = {2013}, month = dec, pages = |
|
{3851–3873}} |
|
- >- |
|
@article{Larance2016, title = {Global Membrane Protein Interactome Analysis |
|
using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation |
|
Profiling}, volume = {15}, ISSN = {1535-9476}, url = |
|
{http://dx.doi.org/10.1074/mcp.O115.055467}, DOI = {10.1074/mcp.o115.055467}, |
|
number = {7}, journal = {Molecular & Cellular Proteomics}, publisher = |
|
{Elsevier BV}, author = {Larance, Mark and Kirkwood, Kathryn J. and Tinti, |
|
Michele and Brenes Murillo, Alejandro and Ferguson, Michael A.J. and |
|
Lamond, Angus I.}, year = {2016}, month = jul, pages = {2476–2490}} |
|
- >- |
|
@article{Mallam2019, title = {Systematic Discovery of Endogenous Human |
|
Ribonucleoprotein Complexes}, volume = {29}, ISSN = {2211-1247}, url = |
|
{http://dx.doi.org/10.1016/j.celrep.2019.09.060}, DOI = |
|
{10.1016/j.celrep.2019.09.060}, number = {5}, journal = {Cell Reports}, |
|
publisher = {Elsevier BV}, author = {Mallam, Anna L. and Sae-Lee, Wisath and |
|
Schaub, Jeffrey M. and Tu, Fan and Battenhouse, Anna and Jang, Yu Jin and |
|
Kim, Jonghwan and Wallingford, John B. and Finkelstein, Ilya J. and |
|
Marcotte, Edward M. and Drew, Kevin}, year = {2019}, month = oct, pages = |
|
{1351--1368.e5}} |
|
- >- |
|
@article{Moutaoufik2019, title = {Rewiring of the Human Mitochondrial |
|
Interactome during Neuronal Reprogramming Reveals Regulators of the |
|
Respirasome and Neurogenesis}, volume = {19}, ISSN = {2589-0042}, url = |
|
{http://dx.doi.org/10.1016/j.isci.2019.08.057}, DOI = |
|
{10.1016/j.isci.2019.08.057}, journal = {iScience}, publisher = {Elsevier BV}, |
|
author = {Moutaoufik, Mohamed Taha and Malty, Ramy and Amin, Shahreen and |
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Zhang, Qingzhou and Phanse, Sadhna and Gagarinova, Alla and Zilocchi, Mara |
|
and Hoell, Larissa and Minic, Zoran and Gagarinova, Maria and Aoki, |
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Hiroyuki and Stockwell, Jocelyn and Jessulat, Matthew and Goebels, Florian |
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and Broderick, Kirsten and Scott, Nichollas E. and Vlasblom, James and |
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Musso, Gabriel and Prasad, Bhanu and Lamantea, Eleonora and Garavaglia, |
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Barbara and Rajput, Alex and Murayama, Kei and Okazaki, Yasushi and |
|
Foster, Leonard J. and Bader, Gary D. and Cayabyab, Francisco S. and Babu, |
|
Mohan}, year = {2019}, month = sep, pages = {1114–1132}} |
|
- >- |
|
@article{Wan2015, title = {Panorama of ancient metazoan macromolecular |
|
complexes}, volume = {525}, ISSN = {1476-4687}, url = |
|
{http://dx.doi.org/10.1038/nature14877}, DOI = {10.1038/nature14877}, number = |
|
{7569}, journal = {Nature}, publisher = {Springer Science and Business Media |
|
LLC}, author = {Wan, Cuihong and Borgeson, Blake and Phanse, Sadhna and |
|
Tu, Fan and Drew, Kevin and Clark, Greg and Xiong, Xuejian and Kagan, |
|
Olga and Kwan, Julian and Bezginov, Alexandr and Chessman, Kyle and Pal, |
|
Swati and Cromar, Graham and Papoulas, Ophelia and Ni, Zuyao and Boutz, |
|
Daniel R. and Stoilova, Snejana and Havugimana, Pierre C. and Guo, Xinghua |
|
and Malty, Ramy H. and Sarov, Mihail and Greenblatt, Jack and Babu, Mohan |
|
and Derry, W. Brent and R. Tillier, Elisabeth and Wallingford, John B. and |
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Parkinson, John and Marcotte, Edward M. and Emili, Andrew}, year = {2015}, |
|
month = sep, pages = {339–344}} |
|
citation_apa: |
|
- >- |
|
Connelly, K. E., Hedrick, V., Paschoal Sobreira, T. J., Dykhuizen, E. C., & |
|
Aryal, U. K. (2018). Analysis of Human Nuclear Protein Complexes by |
|
Quantitative Mass Spectrometry Profiling. Proteomics, 18(11), e1700427. |
|
https://doi.org/10.1002/pmic.201700427 |
|
- Kirkwood, K. J., Ahmad, Y., Larance, M., & Lamond, A. I. (2013). Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. Molecular & cellular proteomics: MCP, 12(12), 3851–3873. https://doi.org/10.1074/mcp.M113.032367 |
|
- Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. A., & Lamond, A. I. (2016). Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. Molecular & cellular proteomics: MCP, 15(7), 2476–2490. https://doi.org/10.1074/mcp.O115.055467 |
|
- >- |
|
Mallam, A. L., Sae-Lee, W., Schaub, J. M., Tu, F., Battenhouse, A., Jang, Y. |
|
J., Kim, J., Wallingford, J. B., Finkelstein, I. J., Marcotte, E. M., & Drew, |
|
K. (2019). Systematic Discovery of Endogenous Human Ribonucleoprotein |
|
Complexes. Cell reports, 29(5), 1351–1368.e5. |
|
https://doi.org/10.1016/j.celrep.2019.09.060 |
|
- >- |
|
Moutaoufik, M. T., Malty, R., Amin, S., Zhang, Q., Phanse, S., Gagarinova, A., |
|
Zilocchi, M., Hoell, L., Minic, Z., Gagarinova, M., Aoki, H., Stockwell, J., |
|
Jessulat, M., Goebels, F., Broderick, K., Scott, N. E., Vlasblom, J., Musso, |
|
G., Prasad, B., Lamantea, E., … Babu, M. (2019). Rewiring of the Human |
|
Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of |
|
the Respirasome and Neurogenesis. iScience, 19, 1114–1132. |
|
https://doi.org/10.1016/j.isci.2019.08.057 |
|
- >- |
|
Wan, C., Borgeson, B., Phanse, S., Tu, F., Drew, K., Clark, G., Xiong, X., |
|
Kagan, O., Kwan, J., Bezginov, A., Chessman, K., Pal, S., Cromar, G., |
|
Papoulas, O., Ni, Z., Boutz, D. R., Stoilova, S., Havugimana, P. C., Guo, X., |
|
Malty, R. H., … Emili, A. (2015). Panorama of ancient metazoan macromolecular |
|
complexes. Nature, 525(7569), 339–344. https://doi.org/10.1038/nature14877 |
|
--- |
|
|
|
|
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# CF/MS Elution Profile PPI Dataset |
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|
|
Includes processed data from several *Homo sapiens* protein co-fractionation mass spectrometry (CF/MS) experiments, as well as positive/negative protein-protein interaction (PPI) labels for each pair. |
|
|
|
Collated, maintained by **Drew Lab at University of Illinois at Chicago** |
|
|
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[Drew Lab webpage](https://ksdrew.github.io/) |
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|
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## File structure |
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- The **.elut** files each contain a collection elution traces for proteins from a given CF/MS experiment. These can be paired to make sample data. A complete list of data sources can be found at the bottom of this README |
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- The **.txt** files contain line-wise specification of protein complexes used to generate positive/negative labels. These can be used to direct the pairing of elution traces into data points. |
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- **intact_complex_merge_20230309.train_ppis.txt**: List of positive PPIs for training data |
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- **intact_complex_merge_20230309.test_ppis.txt**: List of positive PPIs for testing data |
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- **intact_complex_merge_20230309.neg_train_ppis.txt**: List of negative PPIs for training data |
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- **intact_complex_merge_20230309.neg_test_ppis.txt**: List of negative PPIs for testing data |
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- **intact_complex_merge_20230309.train.txt** Line-wise list of protein complexes |
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### List of publications/experiments from which this dataset was assembled: |
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|
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Connelly, K. E., Hedrick, V., Paschoal Sobreira, T. J., Dykhuizen, E. C., & Aryal, U. K. (2018). Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry Profiling. Proteomics, 18(11), e1700427. https://doi.org/10.1002/pmic.201700427 |
|
- T98G_glioblastoma_multiforme_cells_SEC_Conelly_2018_Bio1.elut |
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- T98G_glioblastoma_multiforme_cells_SEC_Conelly_2018_Bio2.elut |
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|
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Kirkwood, K. J., Ahmad, Y., Larance, M., & Lamond, A. I. (2013). Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. Molecular & cellular proteomics : MCP, 12(12), 3851–3873. https://doi.org/10.1074/mcp.M113.032367 |
|
- U2OS_cells_SEC_Kirkwood_2013_rep1.elut |
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- U2OS_cells_SEC_Kirkwood_2013_rep2.elut |
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- U2OS_cells_SEC_Kirkwood_2013_rep3.elut |
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|
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Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. A., & Lamond, A. I. (2016). Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. Molecular & cellular proteomics : MCP, 15(7), 2476–2490. https://doi.org/10.1074/mcp.O115.055467 |
|
- U2OS_cells_SEC_Larance_2016_PT3281S1.elut |
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- U2OS_cells_SEC_Larance_2016_PT3441S1.elut |
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- U2OS_cells_SEC_Larance_2016_PT3442S1.elut |
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- U2OS_cells_SEC_Larance_2016_PT3701S1.elut |
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- U2OS_cells_SEC_Larance_2016_PTSS3801.elut |
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- U2OS_cells_SEC_Larance_2016_PTSS3802.elut |
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|
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Mallam, A. L., Sae-Lee, W., Schaub, J. M., Tu, F., Battenhouse, A., Jang, Y. J., Kim, J., Wallingford, J. B., Finkelstein, I. J., Marcotte, E. M., & Drew, K. (2019). Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell reports, 29(5), 1351–1368.e5. https://doi.org/10.1016/j.celrep.2019.09.060 |
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- HEK_293_T_cells_SEC_Mallam_2019_C1.elut |
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- HEK_293_T_cells_SEC_Mallam_2019_C2.elut |
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|
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Moutaoufik, M. T., Malty, R., Amin, S., Zhang, Q., Phanse, S., Gagarinova, A., Zilocchi, M., Hoell, L., Minic, Z., Gagarinova, M., Aoki, H., Stockwell, J., Jessulat, M., Goebels, F., Broderick, K., Scott, N. E., Vlasblom, J., Musso, G., Prasad, B., Lamantea, E., … Babu, M. (2019). Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis. iScience, 19, 1114–1132. https://doi.org/10.1016/j.isci.2019.08.057 |
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- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_2_R1.elut |
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- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_2_R2.elut |
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- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_R1.elut |
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- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_R2.elut |
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- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_2_R1.elut |
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- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_2_R2.elut |
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- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_R1.elut |
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- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_R2.elut |
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Wan, C., Borgeson, B., Phanse, S., Tu, F., Drew, K., Clark, G., Xiong, X., Kagan, O., Kwan, J., Bezginov, A., Chessman, K., Pal, S., Cromar, G., Papoulas, O., Ni, Z., Boutz, D. R., Stoilova, S., Havugimana, P. C., Guo, X., Malty, R. H., … Emili, A. (2015). Panorama of ancient metazoan macromolecular complexes. Nature, 525(7569), 339–344. https://doi.org/10.1038/nature14877 |
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- CB660_neural_stem_cell_IEX_Wan_2015.elut |
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- G166_glioma_stem_cell_IEX_Wan_2015_Hs_HCW_2.elut |
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- G166_glioma_stem_cell_IEX_Wan_2015_Hs_HCW_3.elut |
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- IEX_Wan_2015_Hs_HCW_4.elut |
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- IEX_Wan_2015_Hs_HCW_5.elut |
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- IEX_Wan_2015_Hs_HCW_6.elut |
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- IEX_Wan_2015_Hs_HCW_7.elut |
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- IEX_Wan_2015_Hs_HCW_8.elut |
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- IEX_Wan_2015_Hs_HCW_9.elut |
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- IEX_Wan_2015_Hs_IEX_1.elut |
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- IEX_Wan_2015_Hs_IEX_2.elut |
