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Mass Spectrometry

  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Covington B, Seyedsayamdost M. Guidelines for metabolomics-guided transposon mutagenesis for microbial natural product discovery. Methods Enzymol. 2022;665:305–323. PMCID: PMC9078877
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Kleiner R. Interrogating the transcriptome with metabolically incorporated ribonucleosides. Mol Omics. 2021;17(6):833–841. PMCID: PMC8648987
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Murray L, Combs A, Rekapalli P, Cristea I. Methods for characterizing protein acetylation during viral infection. Methods Enzymol. 2019;626:587–620. PMCID: PMC6889803
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Su X, Lu W, Rabinowitz J. Metabolite Spectral Accuracy on Orbitraps. Anal Chem. 2017;89(11):5940–5948. PMCID: PMC5748891
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Jang C, Chen L, Rabinowitz J. Metabolomics and Isotope Tracing. Cell. 2018;173(4):822–837. PMCID: PMC6034115
    Reference Link
  • 1.
    Baars O, Zhang X, Morel F, Seyedsayamdost M. The Siderophore Metabolome of Azotobacter vinelandii. Appl Environ Microbiol. 2016;82(1):27–39. PMCID: PMC4702634
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Carabetta V, Cristea I. Regulation, Function, and Detection of Protein Acetylation in Bacteria. J Bacteriol. 2017;199(16). PMCID: PMC5527388
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Greco T, Cristea I. Proteomics Tracing the Footsteps of Infectious Disease. Mol Cell Proteomics. 2017;16(4 suppl 1):S5-S14. PMCID: PMC5393401
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    Lin K, Zakian V. 21st Century Genetics: Mass Spectrometry of Yeast Telomerase. Cold Spring Harb Symp Quant Biol. 2015;80:111–6. PMCID: PMC5441543
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link
  • 1.
    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
    Reference Link

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