Papers
1) McKee, C. M., Cranston, M., McKay, E. C., Arefian, M., Mawhinney, T. J., Collins, B. C. & Coll, R. C. Induced pluripotent stem cell-derived macrophages as a model for human inflammasome signaling. bioRxiv (2025) https://doi.org/10.1101/2025.09.05.674456
2) Rosenberger, G., Xue, P., Bludau, I., Martelli, C., Williams, E., Collins, B. C., Califano, A., Liu, Y. & Aebersold, R. Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability. bioRxiv (2025) https://doi.org/10.1101/2025.09.25.678633
3) Banaei-Esfahani, A., Farnov, S. B., Trauner, A., Gygli, S. M., Rustad, T. R., Feldmann, J., Gillet, L. C., Schubert, O. T., Beisel, C., Sherman, D. R., Aebersold, R., Gagneux, S. & Collins, B. C. Rv1985c-Driven Transcriptional Network Rewiring Underlies Lineage-Specific Phenotypes in Mycobacterium tuberculosis. bioRxiv 2020.02.14.943365 (2025) https://doi.org/10.1101/2020.02.14.943365
4) Kusejko, K., Arefian, M., Duroux, D., Zeeb, M., Dollé, C., Hoffmann, M., Labhardt, N., Wandeler, G., Cavassini, M., Haller, S., Bernasconi, E., Russenberger, D., Kouyos, R. D., Günthard, H. F., Collins, B. C., Nemeth, J. & the Swiss HIV Cohort Study. Inflammation and B cell activation define a plasma proteome signature predicting tuberculosis in people with HIV. mBio 0, e01585–25 (2025) https://doi.org/10.1128/mbio.01585-25
5) Searle, B. C., Chazarin, B., Collins, B. C., Kundu, D. J., Huang, S., Lin, Q., Liu, Y., Low, T. Y., Saba, J., Guo, T., Palmisano, G. & Fert-Bober, J. Advancing Scientific Communication in Proteomics. Journal of Proteome Research 24, 381–382 (2025) https://doi.org/10.1021/acs.jproteome.4c01098
6) Yue, L., Jiang, W., Li, S., Luo, M., Fan, N., Zhan, X., Chen, K., Lu, T., Guo, F., Li, D., Ge, W., Nie, Z., Lyu, M., Jun, A., Wang, Y., Chen, Y., Fu, Z., Xiang, N., Li, L., Yu, F., Teo, G. C., Nesvizhskii, A. I., Wang, M., Snyder, M. P., Collins, B., Aebersold, R., Xu, F., Zhu, Y., Liu, T., Li, Y. & Guo, T. Spatial distribution of the proteome in human body and cancers. bioRxiv 2025.02.14.638212 (2025) https://doi.org/10.1101/2025.02.14.638212
7) Cheema, S. K., Grimwade-Mann, M., Weaver, G., Collins, B., Shenker, N. & Cameron, S. Freeze-drying donor human milk allows compositional stability for 12 months at ambient temperatures. Journal of Food Composition and Analysis 137, 106936 (2025) https://doi.org/10.1016/j.jfca.2024.106936
8) He, F., Aebersold, R., Baker, M. S., Bian, X., Bo, X., Chan, D. W., Chang, C., Chen, L., Chen, X., Chen, Y.-J., Cheng, H., Collins, B. C., Corrales, F., Cox, J., E, W., Van Eyk, J. E., Fan, J., Faridi, P., Figeys, D., Gao, G. F., Gao, W., Gao, Z.-H., Goda, K., Goh, W. W. B., Gu, D., Guo, C., Guo, T., He, Y., Heck, A. J. R., Hermjakob, H., Hunter, T., Iyer, N. G., Jiang, Y., Jimenez, C. R., Joshi, L., Kelleher, N. L., Li, M., Li, Y., Lin, Q., Liu, C. H., Liu, F., Liu, G.-H., Liu, Y., Liu, Z., Low, T. Y., Lu, B., Mann, M., Meng, A., Moritz, R. L., Nice, E., Ning, G., Omenn, G. S., Overall, C. M., Palmisano, G., Peng, Y., Pineau, C., Poon, T. C. W., Purcell, A. W., Qiao, J., Reddel, R. R., Robinson, P. J., Roncada, P., Sander, C., Sha, J., Song, E., Srivastava, S., Sun, A., Sze, S. K., Tang, C., Tang, L., Tian, R., Vizcaíno, J. A., Wang, C., Wang, C., Wang, X., Wang, X., Wang, Y., Weiss, T., Wilhelm, M., Winkler, R., Wollscheid, B., Wong, L., Xie, L., Xie, W., Xu, T., Xu, T., Yan, L., Yang, J., Yang, X., Yates, J., Yun, T., Zhai, Q., Zhang, B., Zhang, H., Zhang, L., Zhang, L., Zhang, P., Zhang, Y., Zheng, Y. Z., Zhong, Q. & Zhu, Y. Π-HuB: The proteomic navigator of the human body. Nature 636, 322–331 (2024) https://doi.org/10.1038/s41586-024-08280-5
9) Tonry, C., Linden, K., Collier, P., Ledwidge, M., McDonald, K., Collins, B. C. & Watson, C. J. Proteomic Characterisation of Heart Failure Reveals a Unique Molecular Phenotype for Hypertrophic Cardiomyopathy. Biomedicines 12, 1712 (2024) https://doi.org/10.3390/biomedicines12081712
10) Bludau, I., Nicod, C., Martelli, C., Xue, P., Heusel, M., Fossati, A., Uliana, F., Frommelt, F., Aebersold, R. & Collins, B. C. Rapid Profiling of Protein Complex Reorganization in Perturbed Systems. Journal of Proteome Research 22, 1520–1536 (2023) https://doi.org/10.1021/acs.jproteome.3c00125
11) Penny, J., Arefian, M., Schroeder, G. N., Bengoechea, J. A. & Collins, B. C. A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation. PROTEOMICS 23, 2200038 (2023) https://doi.org/10.1002/pmic.202200038
12) Schreiber, A., Collins, B. C., Davis, C., Enchev, R. I., Sedra, A., D’Antuono, R., Aebersold, R. & Peter, M. Multilayered regulation of autophagy by the Atg1 kinase orchestrates spatial and temporal control of autophagosome formation. Molecular Cell 81, 5066–5081.e10 (2021) https://doi.org/10.1016/j.molcel.2021.10.024
13) Meier-Abt, F., Lu, J., Cannizzaro, E., Pohly, M. F., Kummer, S., Pfammatter, S., Kunz, L., Collins, B. C., Nadeu, F., Lee, K. S., Xue, P., Gwerder, M., Roiss, M., Hüllein, J., Scheinost, S., Dietrich, S., Campo, E., Huber, W., Aebersold, R. & Zenz, T. The protein landscape of chronic lymphocytic leukemia. Blood 138, 2514–2525 (2021) https://doi.org/10.1182/blood.2020009741
14) Trauner, A., Banaei-Esfahani, A., Gygli, S. M., Warmer, P., Feldmann, J., Zampieri, M., Borrell, S., Collins, B. C., Beisel, C., Aebersold, R. & Gagneux, S. Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance. Antimicrobial Agents and Chemotherapy 65, e0050421 (2021) https://doi.org/10.1128/AAC.00504-21
15) Čuklina, J., Lee, C. H., Williams, E. G., Sajic, T., Collins, B. C., Martínez, M. R., Sharma, V. S., Wendt, F., Goetze, S., Keele, G. R., Wollscheid, B., Aebersold, R. & Pedrioli, P. G. A. Diagnostics and correction of batch effects in large-scale proteomic studies: A tutorial. Molecular Systems Biology 17, e10240 (2021) https://doi.org/10.15252/msb.202110240
16) Bludau, I., Frank, M., Dörig, C., Cai, Y., Heusel, M., Rosenberger, G., Picotti, P., Collins, B. C., Röst, H. & Aebersold, R. Systematic detection of functional proteoform groups from bottom-up proteomic datasets. Nature Communications 12, 3810 (2021) https://doi.org/10.1038/s41467-021-24030-x
17) Mori, M., Zhang, Z., Banaei-Esfahani, A., Lalanne, J.-B., Okano, H., Collins, B. C., Schmidt, A., Schubert, O. T., Lee, D.-S., Li, G.-W., Aebersold, R., Hwa, T. & Ludwig, C. From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions. Molecular Systems Biology 17, e9536 (2021) https://doi.org/10.15252/msb.20209536
18) Fossati, A., Frommelt, F., Uliana, F., Martelli, C., Vizovisek, M., Gillet, L., Collins, B., Gstaiger, M. & Aebersold, R. System-Wide Profiling of Protein Complexes Via Size Exclusion Chromatography–Mass SpectrometryMass spectrometry (SEC–MS). in Shotgun Proteomics: Methods and Protocols (eds. Carrera, M. & Mateos, J.) 269–294 (Springer US, 2021). https://doi.org/10.1007/978-1-0716-1178-4_18
19) Rosenberger, G., Heusel, M., Bludau, I., Collins, B. C., Martelli, C., Williams, E. G., Xue, P., Liu, Y., Aebersold, R. & Califano, A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Systems 11, 589–607.e8 (2020) https://doi.org/10.1016/j.cels.2020.11.006
20) Meier, F., Brunner, A.-D., Frank, M., Ha, A., Bludau, I., Voytik, E., Kaspar-Schoenefeld, S., Lubeck, M., Raether, O., Bache, N., Aebersold, R., Collins, B. C., Röst, H. L. & Mann, M. diaPASEF: Parallel accumulation–serial fragmentation combined with data-independent acquisition. Nature Methods 17, 1229–1236 (2020) https://doi.org/10.1038/s41592-020-00998-0
21) Bludau, I., Heusel, M., Frank, M., Rosenberger, G., Hafen, R., Banaei-Esfahani, A., Drogen, A. van, Collins, B. C., Gstaiger, M. & Aebersold, R. Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. Nature Protocols 1–47 (2020) https://doi.org/10.1038/s41596-020-0332-6
22) Heusel, M., Frank, M., Köhler, M., Amon, S., Frommelt, F., Rosenberger, G., Bludau, I., Aulakh, S., Linder, M. I., Liu, Y., Collins, B. C., Gstaiger, M., Kutay, U. & Aebersold, R. A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Systems 10, 133–155.e6 (2020) https://doi.org/10.1016/j.cels.2020.01.001
23) Shao, W., Guo, T., Toussaint, N. C., Xue, P., Wagner, U., Li, L., Charmpi, K., Zhu, Y., Wu, J., Buljan, M., Sun, R., Rutishauser, D., Hermanns, T., Fankhauser, C. D., Poyet, C., Ljubicic, J., Rupp, N., Rüschoff, J. H., Zhong, Q., Beyer, A., Ji, J., Collins, B. C., Liu, Y., Rätsch, G., Wild, P. J. & Aebersold, R. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications 10, 2524 (2019) https://doi.org/10.1038/s41467-019-10513-5
24) Heusel, M., Bludau, I., Rosenberger, G., Hafen, R., Frank, M., Banaei‐Esfahani, A., Drogen, A. van, Collins, B. C., Gstaiger, M. & Aebersold, R. Complex‐centric proteome profiling by SEC‐SWATH‐MS. Molecular Systems Biology 15, e8438 (2019) https://doi.org/10.15252/msb.20188438
25) Collins, B. C. & Aebersold, R. Proteomics goes parallel. Nature Biotechnology 36, 1051–1053 (2018) https://doi.org/10.1038/nbt.4288
26) Ludwig, C., Gillet, L., Rosenberger, G., Amon, S., Collins, B. C. & Aebersold, R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: A tutorial. Molecular Systems Biology 14, e8126 (2018) https://doi.org/10.15252/msb.20178126
27) Hülsmann, J., Kravic, B., Weith, M., Gstaiger, M., Aebersold, R., Collins, B. C. & Meyer, H. AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation. Molecular & Cellular Proteomics 17, 1295–1307 (2018) https://doi.org/10.1074/mcp.RA117.000471
28) Nicod, C., Banaei-Esfahani, A. & Collins, B. C. Elucidation of host–pathogen protein–protein interactions to uncover mechanisms of host cell rewiring. Current Opinion in Microbiology 39, 7–15 (2017) https://doi.org/10.1016/j.mib.2017.07.005
29) Banaei-Esfahani, A., Nicod, C., Aebersold, R. & Collins, B. C. Systems proteomics approaches to study bacterial pathogens: Application to Mycobacterium tuberculosis. Current Opinion in Microbiology 39, 64–72 (2017) https://doi.org/10.1016/j.mib.2017.09.013
30) Rosenberger, G., Bludau, I., Schmitt, U., Heusel, M., Hunter, C. L., Liu, Y., MacCoss, M. J., MacLean, B. X., Nesvizhskii, A. I., Pedrioli, P. G. A., Reiter, L., Röst, H. L., Tate, S., Ting, Y. S., Collins, B. C. & Aebersold, R. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature Methods 14, 921–927 (2017) https://doi.org/10.1038/nmeth.4398
31) Collins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A.-C., Held, J. M., Hirayama-Kurogi, M., Hou, G., Krisp, C., Larsen, B., Lin, L., Liu, S., Molloy, M. P., Moritz, R. L., Ohtsuki, S., Schlapbach, R., Selevsek, N., Thomas, S. N., Tzeng, S.-C., Zhang, H. & Aebersold, R. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communications 8, 291 (2017) https://doi.org/10.1038/s41467-017-00249-5
32) Cortes, T., Schubert, O. T., Banaei-Esfahani, A., Collins, B. C., Aebersold, R. & Young, D. B. Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival. Scientific Reports 7, 8208 (2017) https://doi.org/10.1038/s41598-017-08306-1
33) Schubert, O. T., Röst, H. L., Collins, B. C., Rosenberger, G. & Aebersold, R. Quantitative proteomics: Challenges and opportunities in basic and applied research. Nature Protocols 12, 1289–1294 (2017) https://doi.org/10.1038/nprot.2017.040
34) Rosenberger, G., Liu, Y., Röst, H. L., Ludwig, C., Buil, A., Bensimon, A., Soste, M., Spector, T. D., Dermitzakis, E. T., Collins, B. C., Malmström, L. & Aebersold, R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nature Biotechnology 35, nbt.3908 (2017) https://doi.org/10.1038/nbt.3908
35) Nemeth, J., Vongrad, V., Metzner, K. J., Strouvelle, V. P., Weber, R., Pedrioli, P., Aebersold, R., Günthard, H. F. & Collins, B. C. In Vivo and in Vitro Proteome Analysis of Human Immunodeficiency Virus (HIV)-1-infected, Human CD4+ T Cells. Molecular & Cellular Proteomics 16, S108–S123 (2017) https://doi.org/10.1074/mcp.M116.065235
36) Caron, E., Roncagalli, R., Hase, T., Wolski, W. E., Choi, M., Menoita, M. G., Durand, S., García-Blesa, A., Fierro-Monti, I., Sajic, T., Heusel, M., Weiss, T., Malissen, M., Schlapbach, R., Collins, B. C., Ghosh, S., Kitano, H., Aebersold, R., Malissen, B. & Gstaiger, M. Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports 18, 3219–3226 (2017) https://doi.org/10.1016/j.celrep.2017.03.019
37) Großeholz, R., Koh, C.-C., Veith, N., Fiedler, T., Strauss, M., Olivier, B., Collins, B. C., Schubert, O. T., Bergmann, F., Kreikemeyer, B., Aebersold, R. & Kummer, U. Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis. npj Systems Biology and Applications 2, 16017 (2016) https://doi.org/10.1038/npjsba.2016.17
38) Röst, H. L., Liu, Y., D’Agostino, G., Zanella, M., Navarro, P., Rosenberger, G., Collins, B. C., Gillet, L., Testa, G., Malmström, L. & Aebersold, R. TRIC: An automated alignment strategy for reproducible protein quantification in targeted proteomics. Nature Methods 13, 777–783 (2016) https://doi.org/10.1038/nmeth.3954
39) Aebersold, R., Bensimon, A., Collins, B. C., Ludwig, C. & Sabido, E. Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH. PROTEOMICS 16, 2065–2067 (2016) https://doi.org/10.1002/pmic.201600203
40) Teo, G., Kim, S., Tsou, C.-C., Collins, B., Gingras, A.-C., Nesvizhskii, A. I. & Choi, H. mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry. Journal of Proteomics 129, 108–120 (2015) https://doi.org/10.1016/j.jprot.2015.09.013
41) Parker, S. J., Rost, H., Rosenberger, G., Collins, B. C., Malmström, L., Amodei, D., Venkatraman, V., Raedschelders, K., Eyk, J. E. V. & Aebersold, R. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry. Molecular & Cellular Proteomics 14, 2800–2813 (2015) https://doi.org/10.1074/mcp.O114.042267
42) Marcon, E., Jain, H., Bhattacharya, A., Guo, H., Phanse, S., Pu, S., Byram, G., Collins, B. C., Dowdell, E., Fenner, M., Guo, X., Hutchinson, A., Kennedy, J. J., Krastins, B., Larsen, B., Lin, Z.-Y., Lopez, M. F., Loppnau, P., Miersch, S., Nguyen, T., Olsen, J. B., Paduch, M., Ravichandran, M., Seitova, A., Vadali, G., Vogelsang, M. S., Whiteaker, J. R., Zhong, G., Zhong, N., Zhao, L., Aebersold, R., Arrowsmith, C. H., Emili, A., Frappier, L., Gingras, A.-C., Gstaiger, M., Paulovich, A. G., Koide, S., Kossiakoff, A. A., Sidhu, S. S., Wodak, S. J., Gräslund, S., Greenblatt, J. F. & Edwards, A. M. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nature Methods 12, 725–731 (2015) https://doi.org/10.1038/nmeth.3472
43) Schubert, O. T., Ludwig, C., Kogadeeva, M., Zimmermann, M., Rosenberger, G., Gengenbacher, M., Gillet, L. C., Collins, B. C., Röst, H. L., Kaufmann, S. H. E., Sauer, U. & Aebersold, R. Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis. Cell Host & Microbe 18, 96–108 (2015) https://doi.org/10.1016/j.chom.2015.06.001
44) Guo, T., Kouvonen, P., Koh, C. C., Gillet, L. C., Wolski, W. E., Röst, H. L., Rosenberger, G., Collins, B. C., Blum, L. C., Gillessen, S., Joerger, M., Jochum, W. & Aebersold, R. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nature Medicine 21, 407–413 (2015) https://doi.org/10.1038/nm.3807
45) Schubert, O. T., Gillet, L. C., Collins, B. C., Navarro, P., Rosenberger, G., Wolski, W. E., Lam, H., Amodei, D., Mallick, P., MacLean, B. & Aebersold, R. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nature Protocols 10, 426–441 (2015) https://doi.org/10.1038/nprot.2015.015
46) Liu, Y., Buil, A., Collins, B. C., Gillet, L. C., Blum, L. C., Cheng, L.-Y., Vitek, O., Mouritsen, J., Lachance, G., Spector, T. D., Dermitzakis, E. T. & Aebersold, R. Quantitative variability of 342 plasma proteins in a human twin population. Molecular Systems Biology 11, 786 (2015) https://doi.org/10.15252/msb.20145728
47) Rosenberger, G., Koh, C. C., Guo, T., Röst, H. L., Kouvonen, P., Collins, B. C., Heusel, M., Liu, Y., Caron, E., Vichalkovski, A., Faini, M., Schubert, O. T., Faridi, P., Ebhardt, H. A., Matondo, M., Lam, H., Bader, S. L., Campbell, D. S., Deutsch, E. W., Moritz, R. L., Tate, S. & Aebersold, R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data 1, 140031 (2014) https://doi.org/10.1038/sdata.2014.31
48) Liu, Y., Chen, J., Sethi, A., Li, Q. K., Chen, L., Collins, B., Gillet, L. C. J., Wollscheid, B., Zhang, H. & Aebersold, R. Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness. Molecular & Cellular Proteomics 13, 1753–1768 (2014) https://doi.org/10.1074/mcp.M114.038273
49) Röst, H. L., Rosenberger, G., Navarro, P., Gillet, L., Miladinović, S. M., Schubert, O. T., Wolski, W., Collins, B. C., Malmström, J., Malmström, L. & Aebersold, R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology 32, 219–223 (2014) https://doi.org/10.1038/nbt.2841
50) Collins, B. C., Gillet, L. C., Rosenberger, G., Röst, H. L., Vichalkovski, A., Gstaiger, M. & Aebersold, R. Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system. Nature Methods 10, 1246–1253 (2013) https://doi.org/10.1038/nmeth.2703
51) Liu, Y., Hüttenhain, R., Collins, B. & Aebersold, R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Review of Molecular Diagnostics 13, 811–825 (2013) https://doi.org/10.1586/14737159.2013.845089
52) Collins, B. C., Miller, C. A., Sposny, A., Hewitt, P., Wells, M., Gallagher, W. M. & Pennington, S. R. Development of a Pharmaceutical Hepatotoxicity Biomarker Panel Using a Discovery to Targeted Proteomics Approach. Molecular & Cellular Proteomics 11, 394–410 (2012) https://doi.org/10.1074/mcp.M111.016493
53) Ebhardt, H. A., Sabidó, E., Hüttenhain, R., Collins, B. & Aebersold, R. Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate. PROTEOMICS 12, 1185–1193 (2012) https://doi.org/10.1002/pmic.201100543
54) Collins, B. C. & Gallagher, W. M. Focus on Cancer Proteomics 12’13. PROTEOMICS 12, 2065–2066 (2012) https://doi.org/10.1002/pmic.201270084
55) Dasari, S., Chambers, M. C., Codreanu, S. G., Liebler, D. C., Collins, B. C., Pennington, S. R., Gallagher, W. M. & Tabb, D. L. Sequence Tagging Reveals Unexpected Modifications in Toxicoproteomics. Chemical Research in Toxicology 24, 204–216 (2011) https://doi.org/10.1021/tx100275t
56) Lau, T. Y. K., Collins, B. C., Stone, P., Tang, N., Gallagher, W. M. & Pennington, S. R. Absolute Quantification of Toxicological Biomarkers by Multiple Reaction Monitoring. in Drug Safety Evaluation (ed. Gautier, J.-C.) 417–427 (Humana Press, 2011). http://link.springer.com/protocol/10.1007/978-1-60761-849-2_25
57) Collins, B. C., Lau, T. Y. K., Pennington, S. R. & Gallagher, W. M. Differential Proteomics Incorporating iTRAQ Labeling and Multi-dimensional Separations. in Drug Safety Evaluation (ed. Gautier, J.-C.) 369–383 (Humana Press, 2011). http://link.springer.com/protocol/10.1007/978-1-60761-849-2_23
58) Maher, S. G., McDowell, D. T., Collins, B. C., Muldoon, C. M., Gallagher, W. M. & Reynolds, J. V. Serum Proteomic Profiling Reveals That Pretreatment Complement Protein Levels are Predictive of Esophageal Cancer Patient Response to Neoadjuvant Chemoradiation. Annals of Surgery November 2011 254, 809–817 (2011) https://doi.org/10.1097/SLA.0b013e31823699f2
59) Collins, B. C., Sposny, A., McCarthy, D., Brandenburg, A., Woodbury, R., Pennington, S. R., Gautier, J.-C., Hewitt, P. & Gallagher, W. M. Use of SELDI MS to discover and identify potential biomarkers of toxicity in InnoMed PredTox: A multi-site, multi-compound study. PROTEOMICS 10, 1592–1608 (2010) https://doi.org/10.1002/pmic.200900608
60) Collins, B. C., Lau, T. Y. K., O’Connor, D. P. & Hondermarck, H. Cancer proteomics–an evolving battlefield. Conference on Cancer Proteomics 2009: Mechanistic Insights, Technological Advances & Molecular Medicine. EMBO reports 10, 1202–1205 (2009) https://doi.org/10.1038/embor.2009.222
61) Collins, B. C., Clarke, A., Kitteringham, N. R., Gallagher, W. M. & Pennington, S. R. Use of proteomics for the discovery of early markers of drug toxicity. Expert Opinion on Drug Metabolism & Toxicology 3, 689–704 (2007) https://doi.org/10.1517/17425255.3.5.689