1) 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
2) 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 re-organization in perturbed systems. bioRxiv 2021.12.17.473177 (2021) https://doi.org/10.1101/2021.12.17.473177
3) 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
4) 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
5) 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
6) 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 (CLL). Blood (2021) https://doi.org/10.1182/blood.2020009741
7) 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
8) 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 ChromatographyMass SpectrometryMass spectrometry (SECMS). 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
9) 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
10) 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
11) 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
12) Banaei-Esfahani, A., Trauner, A., Borrell, S., Gygli, S. M., Rustad, T. R., Feldmann, J., Gillet, L. C., Schubert, O. T., Sherman, D. R., Beisel, C., Gagneux, S., Aebersold, R. & Collins, B. C. Network analysis identifies regulators of lineage-specific phenotypes in Mycobacterium tuberculosis. bioRxiv 2020.02.14.943365 (2020) https://doi.org/10.1101/2020.02.14.943365
13) 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
14) 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
15) 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 SECSWATHMS. Molecular Systems Biology 15, e8438 (2019) https://doi.org/10.15252/msb.20188438
16) Collins, B. C. & Aebersold, R. Proteomics goes parallel. Nature Biotechnology 36, 1051–1053 (2018) https://doi.org/10.1038/nbt.4288
17) 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
18) 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
19) 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
20) 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
21) 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
22) 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
23) 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
24) 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
25) 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
26) 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
27) 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
28) 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
29) 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
30) 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
31) 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
32) 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
33) 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
34) 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
35) 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
36) 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
37) 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
38) 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
39) 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
40) 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
41) 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
42) 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
43) Casson, C. & Shin, S. Inflammasome-mediated cell death in response to bacterial pathogens that access the host cell cytosol: Lessons from legionella pneumophila. Frontiers in Cellular and Infection Microbiology 3, 111 (2013) https://doi.org/10.3389/fcimb.2013.00111
44) 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
45) 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
46) Collins, B. C. & Gallagher, W. M. Focus on Cancer Proteomics 12’13. PROTEOMICS 12, 2065–2066 (2012) https://doi.org/10.1002/pmic.201270084
47) 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
48) 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
49) 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
50) 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
51) 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
52) 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
53) 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