Omenn G, Lane L, Overall C, Pineau C, Packer N, Cristea I, Lindskog C, Weintraub S, Orchard S, Roehrl M, Nice E, Liu S, Bandeira N, Chen Y-J, Guo T, Aebersold R, Moritz R, Deutsch E. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res. 2023;22(4):1024–1042. PMCID: PMC10081950

Kennedy M, Tyl M, Betsinger C, Federspiel J, Sheng X, Arbuckle J, Kristie T, Cristea I. A TRUSTED targeted mass spectrometry assay for pan-herpesvirus protein detection. Cell Rep. 2022;39(6):110810. PMCID: PMC9245836

Covington B, Seyedsayamdost M. Guidelines for metabolomics-guided transposon mutagenesis for microbial natural product discovery. Methods Enzymol. 2022;665:305–323. PMCID: PMC9078877

Burton A, Hamza G, Zhang A, Muir T. Chemical biology approaches to study histone interactors. Biochem Soc Trans. 2021;49(5):2431–2441. PMCID: PMC9785950

Omenn G, Lane L, Overall C, Paik Y-K, Cristea I, Corrales F, Lindskog C, Weintraub S, Roehrl M, Liu S, Bandeira N, Srivastava S, Chen Y-J, Aebersold R, Moritz R, Deutsch E. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. J Proteome Res. 2021;20(12):5227–5240. PMCID: PMC9340669

Kleiner R. Interrogating the transcriptome with metabolically incorporated ribonucleosides. Mol Omics. 2021;17(6):833–841. PMCID: PMC8648987

Yoshimura A, Covington B, Gallant Étienne, Zhang C, Li A, Seyedsayamdost M. Unlocking Cryptic Metabolites with Mass Spectrometry-Guided Transposon Mutant Selection. ACS Chem Biol. 2020;15(10):2766–2774. PMCID: PMC7572862

Song B, Liu D, Greco T, Cristea I. Post-translational modification control of viral DNA sensors and innate immune signaling. Adv Virus Res. 2021;109:163–199. PMCID: PMC8489191

Omenn G, Lane L, Overall C, Cristea I, Corrales F, Lindskog C, Paik Y-K, Van Eyk J, Liu S, Pennington S, Snyder M, Baker M, Bandeira N, Aebersold R, Moritz R, Deutsch E. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res. 2020;19(12):4735–4746. PMCID: PMC7718309

Farag M, Hegazi N, Donia M. Molecular networking based LC/MS reveals novel biotransformation products of green coffee by ex vivo cultures of the human gut microbiome. Metabolomics. 2020;16(8):86. PMID: 32748036

Stadlmeier M, Runtsch L, Streshnev F, Wühr M, Carell T. A Click-Chemistry-Based Enrichable Crosslinker for Structural and Protein Interaction Analysis by Mass Spectrometry. Chembiochem. 2020;21(1-2):103–107. PMCID: PMC6980279

Winer B, Edgel K, Zou X, Sellau J, Hadiwidjojo S, Garver L, McDonough C, Kelleher N, Thomas P, Villasante E, Ploss A, Gerbasi V. Identification of Plasmodium falciparum proteoforms from liver stage models. Malar J. 2020;19(1):10. PMCID: PMC6947969

Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871

Federspiel J, Tandon P, Wilczewski C, Wasson L, Herring L, Venkatesh S, Cristea I, Conlon F. Conservation and divergence of protein pathways in the vertebrate heart. PLoS Biol. 2019;17(9):e3000437. PMCID: PMC6750614

Murray L, Combs A, Rekapalli P, Cristea I. Methods for characterizing protein acetylation during viral infection. Methods Enzymol. 2019;626:587–620. PMCID: PMC6889803

Stine R, Sakers A, TeSlaa T, Kissig M, Stine Z, Kwon C, Cheng L, Lim H-W, Kaestner K, Rabinowitz J, Seale P. PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism. Cell Stem Cell. 2019;25(6):830–845.e8. PMCID: PMC6898778

Hashimoto Y, Greco T, Cristea I. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. Adv Exp Med Biol. 2019;1140:143–154. PMID: 31347046

Wang W, Ishibashi J, Trefely S, Shao M, Cowan A, Sakers A, Lim H-W, O’Connor S, Doan M, Cohen P, Baur J, King T, Veech R, Won K-J, Rabinowitz J, Snyder N, Gupta R, Seale P. A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate. Cell Metab. 2019;30(1):174–189.e5. PMCID: PMC6836679

Su X, Lu W, Rabinowitz J. Metabolite Spectral Accuracy on Orbitraps. Anal Chem. 2017;89(11):5940–5948. PMCID: PMC5748891

Federspiel J, Cristea I. Considerations for Identifying Endogenous Protein Complexes from Tissue via Immunoaffinity Purification and Quantitative Mass Spectrometry. Methods Mol Biol. 2019;1977:115–143. PMID: 30980326

Xu F, Wu Y, Zhang C, Davis K, Moon K, Bushin L, Seyedsayamdost M. A genetics-free method for high-throughput discovery of cryptic microbial metabolites. Nat Chem Biol. 2019;15(2):161–168. PMCID: PMC6339573

Arguello E, Srikumar T, Kleiner R. A Photocrosslinking-Based RNA Chemical Proteomics Approach to Profile m A-Regulated Protein-RNA Interactions. Curr Protoc Nucleic Acid Chem. 2018;75(1):e69. PMID: 30408339

Gupta M, Sonnett M, Ryazanova L, Presler M, Wühr M. Quantitative Proteomics of Xenopus Embryos I, Sample Preparation. Methods Mol Biol. 2018;1865:175–194. PMCID: PMC6564683

Sonnett M, Gupta M, Nguyen T, Wühr M. Quantitative Proteomics for Xenopus Embryos II, Data Analysis. Methods Mol Biol. 2018;1865:195–215. PMCID: PMC6534117

Gilbertson S, Federspiel J, Hartenian E, Cristea I, Glaunsinger B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Elife. 2018;7. PMCID: PMC6203436

Jang C, Chen L, Rabinowitz J. Metabolomics and Isotope Tracing. Cell. 2018;173(4):822–837. PMCID: PMC6034115

Baars O, Zhang X, Morel F, Seyedsayamdost M. The Siderophore Metabolome of Azotobacter vinelandii. Appl Environ Microbiol. 2016;82(1):27–39. PMCID: PMC4702634

Baars O, Zhang X, Gibson M, Stone A, Morel F, Seyedsayamdost M. Crochelins: Siderophores with an Unprecedented Iron-Chelating Moiety from the Nitrogen-Fixing Bacterium Azotobacter chroococcum. Angew Chem Int Ed Engl. 2018;57(2):536–541. PMID: 29134779

Aebersold R, Agar J, Amster J, Baker M, Bertozzi C, Boja E, Costello C, Cravatt B, Fenselau C, Garcia B, Ge Y, Gunawardena J, Hendrickson R, Hergenrother P, Huber C, Ivanov A, Jensen O, Jewett M, Kelleher N, Kiessling L, Krogan N, Larsen M, Loo J, Loo R, Lundberg E, MacCoss M, Mallick P, Mootha V, Mrksich M, Muir T, Patrie S, Pesavento J, Pitteri S, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff S, Smith L, Snyder M, Thomas P, Uhlén M, Van Eyk J, Vidal M, Walt D, White F, Williams E, Wohlschlager T, Wysocki V, Yates N, Young N, Zhang B. How many human proteoforms are there?. Nat Chem Biol. 2018;14(3):206–214. PMCID: PMC5837046

Rowland E, Snowden C, Cristea I. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Curr Opin Chem Biol. 2018;42:76–85. PMCID: PMC5965299

Rowland E, Greco T, Snowden C, McCabe A, Silhavy T, Cristea I. Sirtuin Lipoamidase Activity Is Conserved in Bacteria as a Regulator of Metabolic Enzyme Complexes. mBio. 2017;8(5). PMCID: PMC5596343

Chen L, Ducker G, Lu W, Teng X, Rabinowitz J. An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate. Anal Bioanal Chem. 2017;409(25):5955–5964. PMCID: PMC5737010

Lu W, Su X, Klein M, Lewis I, Fiehn O, Rabinowitz J. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem. 2017;86:277–304. PMCID: PMC5734093

Carabetta V, Cristea I. Regulation, Function, and Detection of Protein Acetylation in Bacteria. J Bacteriol. 2017;199(16). PMCID: PMC5527388

Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov A, Moresco J, Blokhina T, Wolle D, Aoki T, Ryabykh V, Yates J, Shidlovskii Y, Georgiev P, Schedl P, Chetverina D. The GAGA factor regulatory network: Identification of GAGA factor associated proteins. PLoS One. 2017;12(3):e0173602. PMCID: PMC5351981

Greco T, Cristea I. Proteomics Tracing the Footsteps of Infectious Disease. Mol Cell Proteomics. 2017;16(4 suppl 1):S5-S14. PMCID: PMC5393401

Digianantonio K, Korolev M, Hecht M. A Non-natural Protein Rescues Cells Deleted for a Key Enzyme in Central Metabolism. ACS Synth Biol. 2017;6(4):694–700. PMID: 28055179

Seyedsayamdost M, Case R, Kolter R, Clardy J. The Jekyll-and-Hyde chemistry of Phaeobacter gallaeciensis. Nat Chem. 2011;3(4):331–5. PMCID: PMC3376411

Futran A, Kyin S, Shvartsman S, Link J. Mapping the binding interface of ERK and transcriptional repressor Capicua using photocrosslinking. Proc Natl Acad Sci U S A. 2015;112(28):8590–5. PMCID: PMC4507193

Wühr M, Haas W, McAlister G, Peshkin L, Rad R, Kirschner M, Gygi S. Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster. Anal Chem. 2012;84(21):9214–21. PMCID: PMC3771681

Wühr M, Freeman R, Presler M, Horb M, Peshkin L, Gygi S, Kirschner M. Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol. 2014;24(13):1467–1475. PMCID: PMC4090281

Lin K-W, McDonald K, Guise A, Chan A, Cristea I, Zakian V. Proteomics of yeast telomerase identified Cdc48-Npl4-Ufd1 and Ufd4 as regulators of Est1 and telomere length. Nat Commun. 2015;6:8290. PMCID: PMC4579843

Lin K, Zakian V. 21st Century Genetics: Mass Spectrometry of Yeast Telomerase. Cold Spring Harb Symp Quant Biol. 2015;80:111–6. PMCID: PMC5441543

Greco T, Guise A, Cristea I. Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy. Methods Mol Biol. 2016;1410:39–63. PMCID: PMC4916643

Schauder S, Shokat K, Surette M, Bassler B. The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule. Mol Microbiol. 2001;41(2):463–76. PMID: 11489131

Xavier K, Miller S, Lu W, Kim J, Rabinowitz J, Pelczer I, Semmelhack M, Bassler B. Phosphorylation and processing of the quorum-sensing molecule autoinducer-2 in enteric bacteria. ACS Chem Biol. 2007;2(2):128–36. PMID: 17274596