README.md

---
size_categories:
- 1M<n<10M
pretty_name: CF/MS Homo sapiens Elution Profile PPI Dataset
tags:
- biology
- chemistry
dataset_summary: >-
  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:
- >-
  @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 &amp; 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 &amp; 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
  Zhang,  Qingzhou and Phanse,  Sadhna and Gagarinova,  Alla and Zilocchi,  Mara
  and Hoell,  Larissa and Minic,  Zoran and Gagarinova,  Maria and Aoki, 
  Hiroyuki and Stockwell,  Jocelyn and Jessulat,  Matthew and Goebels,  Florian
  and Broderick,  Kirsten and Scott,  Nichollas E. and Vlasblom,  James and
  Musso,  Gabriel and Prasad,  Bhanu and Lamantea,  Eleonora and Garavaglia, 
  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
  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
---


# CF/MS Elution Profile PPI Dataset

Proteins are the functional basis of life, but it is often their interactions with other proteins which gives rise to said functions. Therefore, we are often interested in whether two proteins participate in the same *protein complex*, or if they **'co-complex'**. Co-fractionation mass spectrometry (CF/MS) is a high-throughput method for determining whether proteins form complexes. If they do, both proteins will typically separate out into the same fractions, or **'co-elute'**, during column chromatography experiments. As a result, their abundances will be *highly correlated* across all the fractions measured. CF/MS leverages this fact to identify new protein complexes by attempting to statistically correlate the elution profiles of groups of proteins. Typically, we use Pearson correlation coefficient to determine correlation between protein pairs. While this often works quite well, Pearson is a linear function. Current research is exploring whether there are non-linear, higher-order signals between these elution profiles that might have better predictive power than Pearson. As deep learning models excel at estimating non-linear relationships in data, the goal of this dataset is to act as training data for such models, especially **Siamese networks**.

This 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.

Collated, maintained by **Drew Lab at University of Illinois at Chicago**

[Drew Lab webpage](https://ksdrew.github.io/)

## File formats
- **The .elut file**: A **.elut** file is a TSV-like format containing raw count data from a chromatographic fractionation experiment. Each row in a **.elut** file shows the abundance of a single protein across the collected fractions (columns). Generally speaking, these fractions are collected over time. However, different chromatographic columns can separate proteins along different axes. For example, *Size-eclusion chromatography (SEC)* will mostly separate proteins into fractions according to their *size*; *Ion-exchange chromatography (IEX)* will separate them into fractions according to their *charge*. Each file in this dataset comes from one of these two column separation methods and is named accordingly ('...xx_SEC_xx...' / '...xx_IEX_xx...'). We refer to a given protein's (row's) count data across all fractions (columns) as that protein's elution trace or elution profile. To summarize:
  - A given row contains count data for a specific protein 
  - A row's *first column* contains its associated **protein ID**
  - A row's *subsequent columns* contain that protein's count data from the fractionation experiment
  - **Note: The user may notice that the first row in a .elut file is one column longer than subsequent rows. This is because the first row contains row names (protein IDs), and the first column contains column names (fraction IDs). Therefore, cell 'A0' is empty.**

## 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