Create README.md

README.md

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+# CF/MS Elution Profile PPI Dataset
+
+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.
+
+## File structure
+- 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
+- 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.
+  - **intact_complex_merge_20230309.train_ppis.txt**: List of positive PPIs for training data
+  - **intact_complex_merge_20230309.test_ppis.txt**: List of positive PPIs for testing data
+  - **intact_complex_merge_20230309.neg_train_ppis.txt**: List of negative PPIs for training data
+  - **intact_complex_merge_20230309.neg_test_ppis.txt**: List of negative PPIs for testing data
+  - **intact_complex_merge_20230309.train.txt** Line-wise list of protein complexes
+
+
+
+
+### List of publications/experiments from which this dataset was assembled:
+
+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
+- T98G_glioblastoma_multiforme_cells_SEC_Conelly_2018_Bio2.elut
+
+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
+- U2OS_cells_SEC_Kirkwood_2013_rep2.elut
+- U2OS_cells_SEC_Kirkwood_2013_rep3.elut
+
+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
+- U2OS_cells_SEC_Larance_2016_PT3441S1.elut
+- U2OS_cells_SEC_Larance_2016_PT3442S1.elut
+- U2OS_cells_SEC_Larance_2016_PT3701S1.elut
+- U2OS_cells_SEC_Larance_2016_PTSS3801.elut
+- U2OS_cells_SEC_Larance_2016_PTSS3802.elut
+
+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
+- HEK_293_T_cells_SEC_Mallam_2019_C1.elut
+- HEK_293_T_cells_SEC_Mallam_2019_C2.elut
+
+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
+- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_2_R1.elut
+- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_2_R2.elut
+- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_R1.elut
+- NTera2_embryonal_carcinoma_stem_cells_IEX_Moutaoufik_2019_R2.elut
+- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_2_R1.elut
+- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_2_R2.elut
+- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_R1.elut
+- NTera2_embryonal_carcinoma_stem_cells_SEC_Moutaoufik_2019_R2.elut
+
+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
+- CB660_neural_stem_cell_IEX_Wan_2015.elut
+- G166_glioma_stem_cell_IEX_Wan_2015_Hs_HCW_2.elut
+- G166_glioma_stem_cell_IEX_Wan_2015_Hs_HCW_3.elut
+- IEX_Wan_2015_Hs_HCW_4.elut
+- IEX_Wan_2015_Hs_HCW_5.elut
+- IEX_Wan_2015_Hs_HCW_6.elut
+- IEX_Wan_2015_Hs_HCW_7.elut
+- IEX_Wan_2015_Hs_HCW_8.elut
+- IEX_Wan_2015_Hs_HCW_9.elut
+- IEX_Wan_2015_Hs_IEX_1.elut
+- IEX_Wan_2015_Hs_IEX_2.elut
+
+