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1

Optimized Orbitrap HCD for Quantitative Analysis of Phosphopeptides

Yi Zhang, Scott B. Ficarro, Shaojuan Li, Jarrod A. Marto

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2009

Language:

english

File:

PDF, 926 KB

english, 2009

2

Probing the dynamics of O-GlcNAc glycosylation in the brain using quantitative proteomics

Khidekel, Nelly, Ficarro, Scott B, Clark, Peter M, Bryan, Marian C, Swaney, Danielle L, Rexach, Jessica E, Sun, Yi E, Coon, Joshua J, Peters, Eric C, Hsieh-Wilson, Linda C

Journal:

Nature Chemical Biology

Year:

2007

Language:

english

File:

PDF, 664 KB

english, 2007

3

Online Nanoflow Reversed Phase-Strong Anion Exchange-Reversed Phase Liquid Chromatography–Tandem Mass Spectrometry Platform for Efficient and In-Depth Proteome Sequence Analysis of Complex Organisms

Zhou, Feng, Sikorski, Timothy W., Ficarro, Scott B., Webber, James T., Marto, Jarrod A.

Journal:

Analytical Chemistry

Year:

2011

Language:

english

File:

PDF, 1.06 MB

english, 2011

4

Development of Selective Covalent JAK3 Inhibitors

Tan, Li, Akahane, Koshi, McNally, Randall, Reyskens, Kathleen M.S.E, Ficarro, Scott B, Liu, Suhu, Herter-Sprie, Grit S., Koyama, Shohei, Pattison, Michael J., Labella, Katherine M., Johannessen, Liv,

Journal:

Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 2.51 MB

english, 2015

5

mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data

Ficarro, Scott, Alexander, William, Marto, Jarrod

Journal:

Year:

2017

Language:

english

File:

PDF, 7.43 MB

english, 2017

6

A Chemoproteomic Strategy for Direct and Proteome-wide Covalent Inhibitor Target-site Identification

Browne, Christopher Michael, Jiang, Baishan, Ficarro, Scott B, Doctor, Zainab M, Johnson, Jared Lee, Card, Joseph D, Sivakumaren, Sindhu Carmen, Alexander, William M, Yaron, Tomer, Murphy, Charles Jos

Journal:

Journal of the American Chemical Society

Year:

2018

Language:

english

File:

PDF, 1.30 MB

english, 2018

7

multiplierz v2.0: a Python-based ecosystem for shared access and analysis of native mass spectrometry data

Alexander, William M., Ficarro, Scott B., Adelmant, Guillaume, Marto, Jarrod A.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.60 MB

english, 2017

8

A Structure-Guided Approach to Creating Covalent FGFR Inhibitors

Wenjun Zhou, Wooyoung Hur, Ultan McDermott, Amit Dutt, Wa Xian, Scott B. Ficarro, Jianming Zhang, Sreenath V. Sharma, Joan Brugge, Matthew Meyerson, Jeffrey Settleman, Nathanael S. Gray

Journal:

Chemistry & Biology

Year:

2010

Language:

english

File:

PDF, 1.21 MB

english, 2010

9

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor

Kwiatkowski, Nicholas, Zhang, Tinghu, Rahl, Peter B., Abraham, Brian J., Reddy, Jessica, Ficarro, Scott B., Dastur, Anahita, Amzallag, Arnaud, Ramaswamy, Sridhar, Tesar, Bethany, Jenkins, Catherine E.

Journal:

Year:

2014

Language:

english

File:

PDF, 4.35 MB

english, 2014

10

Potent and Selective Covalent Quinazoline Inhibitors of KRAS G12C

Zeng, Mei, Lu, Jia, Li, Lianbo, Feru, Frederic, Quan, Chunshan, Gero, Thomas W., Ficarro, Scott B., Xiong, Yuan, Ambrogio, Chiara, Paranal, Raymond M., Catalano, Marco, Shao, Jay, Wong, Kwok-Kin, Mart

Journal:

Cell Chemical Biology

Year:

2017

Language:

english

File:

PDF, 4.63 MB

english, 2017

11

MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia

Brown, Fiona C., Still, Eric, Koche, Richard P., Yim, Christina Y., Takao, Sumiko, Cifani, Paolo, Reed, Casie, Gunasekera, Shehana, Ficarro, Scott B., Romanienko, Peter, Mark, Willie, McCarthy, Craig,

Journal:

Cancer Discovery

Year:

2018

Language:

english

File:

PDF, 3.63 MB

english, 2018

12

Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway

Kurppa, Kari J., Liu, Yao, To, Ciric, Zhang, Tinghu, Fan, Mengyang, Vajdi, Amir, Knelson, Erik H., Xie, Yingtian, Lim, Klothilda, Cejas, Paloma, Portell, Andrew, Lizotte, Patrick H., Ficarro, Scott B.

Journal:

Year:

2020

File:

PDF, 6.87 MB

2020

13

SRPKIN-1: A Covalent SRPK1/2 Inhibitor that Potently Converts VEGF from Pro-angiogenic to Anti-angiogenic Isoform

Hatcher, John M., Wu, Guowei, Zeng, Chuyue, Zhu, Jie, Meng, Fan, Patel, Sherrina, Wang, Wenqiu, Ficarro, Scott B., Leggett, Alan L., Powell, Chelsea E., Marto, Jarrod A., Zhang, Kang, Ki Ngo, Jacky Ch

Journal:

Cell Chemical Biology

Year:

2018

Language:

english

File:

PDF, 3.26 MB

english, 2018

14

Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors

Zhang, Tinghu, Kwiatkowski, Nicholas, Olson, Calla M, Dixon-Clarke, Sarah E, Abraham, Brian J, Greifenberg, Ann K, Ficarro, Scott B, Elkins, Jonathan M, Liang, Yanke, Hannett, Nancy M, Manz, Theresa,

Journal:

Nature Chemical Biology

Year:

2016

Language:

english

File:

PDF, 2.92 MB

english, 2016

15

Discovery of MFH290: A Potent and Highly Selective Covalent Inhibitor for Cyclin-Dependent Kinase 12/13

Liu, Yao, Hao, Mingfeng, Leggett, Alan, Gao, Yang, Ficarro, Scott B, Che, Jianwei, He, Zhixiang, Olson, Calla, Marto, Jarrod A., Kwiatkowski, nicholas, Zhang, Tinghu, Gray, Nathanael S

Journal:

Journal of Medicinal Chemistry

Year:

2020

File:

PDF, 1.20 MB

2020

16

Identification of the Plasticity-Relevant Fucose-α(1−2)-Galactose Proteome from the Mouse Olfactory Bulb

Murrey, Heather E., Ficarro, Scott B., Krishnamurthy, Chithra, Domino, Steven E., Peters, Eric C., Hsieh-Wilson, Linda C.

Journal:

Year:

2009

Language:

english

File:

PDF, 2.06 MB

english, 2009

17

Autophosphorylation Properties of Inactive and Active JNK2

Pimienta, Genaro, Ficarro, Scott B., Gutierrez, Gustavo J., Bhoumik, Anindita, Peters, Eric C., Ronai, Ze'ev, Pascual, Jaime

Journal:

Year:

2007

Language:

english

File:

PDF, 949 KB

english, 2007

18

Library dependent LC-MS/MS acquisition via mzAPI/Live

Webber, James T., Askenazi, Manor, Ficarro, Scott B., Iglehart, Max A., Marto, Jarrod A.

Journal:

Year:

2013

Language:

english

File:

PDF, 660 KB

english, 2013

19

Targeted Disruption of the PME-1 Gene Causes Loss of Demethylated PP2A and Perinatal Lethality in Mice

Ortega-Gutiérrez, Silvia, Leung, Donmienne, Ficarro, Scott, Peters, Eric C., Cravatt, Benjamin F., Gay, Nick

Journal:

Year:

2008

Language:

english

File:

PDF, 260 KB

english, 2008

20

Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding

Twomey, Edward C., Ji, Zhejian, Wales, Thomas E., Bodnar, Nicholas O., Ficarro, Scott B., Marto, Jarrod A., Engen, John R., Rapoport, Tom A.

Journal:

Year:

2019

Language:

english

File:

PDF, 7.51 MB

english, 2019

21

Discovery of Covalent MKK4/7 Dual Inhibitor

Jiang, Jie, Jiang, Baishan, He, Zhixiang, Ficarro, Scott B., Che, Jianwei, Marto, Jarrod A., Gao, Yang, Zhang, Tinghu, Gray, Nathanael S.

Journal:

Cell Chemical Biology

Year:

2020

File:

PDF, 2.85 MB

2020

22

Genome-scale proteome quantification by DEEP SEQ mass spectrometry

Zhou, Feng, Lu, Yu, Ficarro, Scott B., Adelmant, Guillaume, Jiang, Wenyu, Luckey, C. John, Marto, Jarrod A.

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 3.85 MB

english, 2013

23

Parallel Identification of O -GlcNAc-Modified Proteins from Cell Lysates

Tai, Hwan-Ching, Khidekel, Nelly, Ficarro, Scott B., Peters, Eric C., Hsieh-Wilson, Linda C.

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 62 KB

english, 2004

24

Pharmacological targeting of the pseudokinase Her3

Xie, Ting, Lim, Sang Min, Westover, Kenneth D, Dodge, Michael E, Ercan, Dalia, Ficarro, Scott B, Udayakumar, Durga, Gurbani, Deepak, Tae, Hyun Seop, Riddle, Steven M, Sim, Taebo, Marto, Jarrod A, Jänn

Journal:

Nature Chemical Biology

Year:

2014

Language:

english

File:

PDF, 1.68 MB

english, 2014

25

Hepatic Dysfunction Caused by Consumption of a High-Fat Diet

Soltis, Anthony R., Kennedy, Norman J., Xin, Xiaofeng, Zhou, Feng, Ficarro, Scott B., Yap, Yoon Sing, Matthews, Bryan J., Lauffenburger, Douglas A., White, Forest M., Marto, Jarrod A., Davis, Roger J.

Journal:

Year:

2017

Language:

english

File:

PDF, 13.91 MB

english, 2017

26

Discovery and StructureâActivity Relationship Study of ( Z )-5-Methylenethiazolidin-4-one Derivatives as Potent and Selective Pan-phosphatidylinositol 5-Phosphate 4-Kinase Inhibitors

Manz, Theresa D., Sivakumaren, Sindhu Carmen, Ferguson, Fleur M., Zhang, Tinghu, Yasgar, Adam, Seo, Hyuk-Soo, Ficarro, Scott B., Card, Joseph D., Shim, Hyeseok, Miduturu, Chandrasekhar V., Simeonov, A

Journal:

Journal of Medicinal Chemistry

Year:

2020

File:

PDF, 1.41 MB

2020

27

Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 Å resolution

Qingping Xu, Piotr Kozbial, Daniel McMullan, S. Sri Krishna, Scott M. Brittain, Scott B. Ficarro, Michael DiDonato, Mitchell D. Miller, Polat Abdubek, Herbert L. Axelrod, Hsiu-Ju Chiu, Thomas Clayton,

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 336 KB

english, 2008

28

Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents

Ficarro, Scott B., Biagi, Jessica M., Wang, Jinhua, Scotcher, Jenna, Koleva, Rositsa I., Card, Joseph D., Adelmant, Guillaume, He, Huan, Askenazi, Manor, Marshall, Alan G., Young, Nicolas L., Gray, Na

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2014

Language:

english

File:

PDF, 1.57 MB

english, 2014

29

Glucose-dependent partitioning of arginine to the urea cycle protects Î²-cells from inflammation

Fu, Accalia, Alvarez-Perez, Juan Carlos, Avizonis, Daina, Kin, Tatsuya, Ficarro, Scott B., Choi, Dong Wook, Karakose, Esra, Badur, Mehmet G., Evans, Lindsay, Rosselot, Carolina, Bridon, Gaelle, Bird,

Journal:

Nature Metabolism

Year:

2020

File:

PDF, 11.78 MB

2020

30

Sub1 and RPA Associate with RNA Polymerase II at Different Stages of Transcription

Timothy W. Sikorski, Scott B. Ficarro, John Holik, TaeSoo Kim, Oliver J. Rando, Jarrod A. Marto, Stephen Buratowski

Journal:

Year:

2011

Language:

english

File:

PDF, 1.47 MB

english, 2011

31

Structure and Ubiquitination-Dependent Activation of TANK-Binding Kinase 1

Tu, Daqi, Zhu, Zehua, Zhou, Alicia Y., Yun, Cai-hong, Lee, Kyung-Eun, Toms, Angela V., Li, Yiqun, Dunn, Gavin P., Chan, Edmond, Thai, Tran, Yang, Shenghong, Ficarro, Scott B., Marto, Jarrod A., Jeon,

Journal:

Year:

2013

Language:

english

File:

PDF, 2.05 MB

english, 2013

32

Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells

Lu, Yu, Loh, Yuin-Han, Li, Hu, Cesana, Marcella, Ficarro, Scott B., Parikh, Jignesh R., Salomonis, Nathan, Toh, Cheng-Xu Delon, Andreadis, Stelios T., Luckey, C. John, Collins, James J., Daley, George

Journal:

Year:

2014

Language:

english

File:

PDF, 1.55 MB

english, 2014

33

Rationally Designed Covalent BCL6 Inhibitor That Targets a Tyrosine Residue in the Homodimer Interface

Teng, Mingxing, Ficarro, Scott B., Yoon, Hojong, Che, Jianwei, Zhou, Jing, Fischer, Eric S., Marto, Jarrod A., Zhang, Tinghu, Gray, Nathanael S.

Journal:

ACS Medicinal Chemistry Letters

Year:

2020

File:

PDF, 636 KB

2020

34

Differential contribution of the mitochondrial translation pathway to the survival of diffuse large B-cell lymphoma subsets

Norberg, Erik, Lako, Ana, Chen, Pei-Hsuan, Stanley, Illana A, Zhou, Feng, Ficarro, Scott B, Chapuy, Bjoern, Chen, Linfeng, Rodig, Scott, Shin, Donghyuk, Choi, Dong Wook, Lee, Sangho, Shipp, Margaret A

Journal:

Cell Death & Differentiation

Year:

2016

Language:

english

File:

PDF, 1.18 MB

english, 2016

35

Improved Electrospray Ionization Efficiency Compensates for Diminished Chromatographic Resolution and Enables Proteomics Analysis of Tyrosine Signaling in Embryonic Stem Cells

Ficarro, Scott B., Zhang, Yi, Lu, Yu, Moghimi, Ahmadali R., Askenazi, Manor, Hyatt, Elzbieta, Smith, Eric D., Boyer, Leah, Schlaeger, Thorsten M., Luckey, C. John, Marto, Jarrod A.

Journal:

Analytical Chemistry

Year:

2009

Language:

english

File:

PDF, 4.95 MB

english, 2009

36

The Cyclophilin A–CD147 complex promotes the proliferation and homing of multiple myeloma cells

Zhu, Di, Wang, Zhongqiu, Zhao, Jian-Jun, Calimeri, Teresa, Meng, Jiang, Hideshima, Teru, Fulciniti, Mariateresa, Kang, Yue, Ficarro, Scott B, Tai, Yu-Tzu, Hunter, Zachary, McMilin, Douglas, Tong, Haox

Journal:

Nature Medicine

Year:

2015

Language:

english

File:

PDF, 3.27 MB

english, 2015

37

Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling

Job D. Cardoza, Jignesh R. Parikh, Scott B. Ficarro, Jarrod A. Marto

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2012

Language:

english

File:

PDF, 881 KB

english, 2012

38

Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6

Park, Eunyoung, Kim, Nayoung, Ficarro, Scott B, Zhang, Yi, Lee, Byung Il, Cho, Ahye, Kim, Kihong, Park, Angela K J, Park, Woong-Yang, Murray, Bradley, Meyerson, Matthew, Beroukhim, Rameen, Marto, Jarr

Journal:

Nature Structural and Molecular Biology

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

39

Structural and Biochemical Analyses Reveal the Mechanism of Glutathione S-Transferase Pi 1 Inhibition by the Anti-cancer Compound Piperlongumine

Harshbarger, Wayne, Gondi, Sudershan, Ficarro, Scott B., Hunter, John, Udayakumar, Durga, Gurbani, Deepak, Singer, William, Liu, Yan, Li, Lianbo, Marto, Jarrod A., Westover, Kenneth D.

Journal:

Journal of Biological Chemistry

Year:

2016

Language:

english

File:

PDF, 1.82 MB

english, 2016

40

Structure of a pseudokinase-domain switch that controls oncogenic activation of Jak kinases

Toms, Angela V, Deshpande, Anagha, McNally, Randall, Jeong, Youngjee, Rogers, Julia M, Kim, Chae Un, Gruner, Sol M, Ficarro, Scott B, Marto, Jarrod A, Sattler, Martin, Griffin, James D, Eck, Michael J

Journal:

Nature Structural and Molecular Biology

Year:

2013

Language:

english

File:

PDF, 671 KB

english, 2013

41

Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity

Ferguson, Fleur M., Doctor, Zainab M., Ficarro, Scott B., Browne, Christopher M., Marto, Jarrod A., Johnson, Jared L., Yaron, Tomer M., Cantley, Lewis C., Kim, Nam Doo, Sim, Taebo, Berberich, Matthew

Journal:

Cell Chemical Biology

Year:

2019

Language:

english

File:

PDF, 6.64 MB

english, 2019

42

Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae

Ficarro, Scott B., McCleland, Mark L., Stukenberg, P. Todd, Burke, Daniel J., Ross, Mark M., Shabanowitz, Jeffrey, Hunt, Donald F., White, Forest M.

Journal:

Nature Biotechnology

Year:

2002

Language:

english

File:

PDF, 68 KB

english, 2002

43

CDK9 Regulates AR Promoter Selectivity and Cell Growth through Serine 81 Phosphorylation

Gordon, Vicki, Bhadel, Shriti, Wunderlich, Winfried, Zhang, JoAnn, Ficarro, Scott B., Mollah, Sahana A., Shabanowitz, Jeffrey, Hunt, Donald F., Xenarios, Ioannis, Hahn, William C., Conaway, Mark, Care

Journal:

Molecular Endocrinology

Year:

2010

Language:

english

File:

PDF, 450 KB

english, 2010

44

Exploring the Phosphoproteome with Mass Spectrometry

Peters, Eric, Brock, Ansgar, Ficarro, Scott

Journal:

Mini Reviews in Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 376 KB

english, 2004

45

Overcoming Resistance to the THZ Series of Covalent Transcriptional CDK Inhibitors

Gao, Yang, Zhang, Tinghu, Terai, Hideki, Ficarro, Scott B., Kwiatkowski, Nicholas, Hao, Ming-Feng, Sharma, Bandana, Christensen, Camilla L., Chipumuro, Edmond, Wong, Kwok-kin, Marto, Jarrod A., Hammer

Journal:

Cell Chemical Biology

Year:

2017

Language:

english

File:

PDF, 3.23 MB

english, 2017

46

Crystal Structure of a Coiled-Coil Domain from Human ROCK I

Tu, Daqi, Li, Yiqun, Song, Hyun Kyu, Toms, Angela V., Gould, Christopher J., Ficarro, Scott B., Marto, Jarrod A., Goode, Bruce L., Eck, Michael J., Kursula, Petri

Journal:

Year:

2011

Language:

english

File:

PDF, 2.27 MB

english, 2011

47

Development of a covalent inhibitor of gut bacterial bile salt hydrolases

Adhikari, Arijit A., Seegar, Tom C. M., Ficarro, Scott B., McCurry, Megan D., Ramachandran, Deepti, Yao, Lina, Chaudhari, Snehal N., Ndousse-Fetter, Sula, Banks, Alexander S., Marto, Jarrod A., Blackl

Journal:

Nature Chemical Biology

Year:

2020

File:

PDF, 4.81 MB

2020

48

A Small Covalent Allosteric Inhibitor of Human Cytomegalovirus DNA Polymerase Subunit Interactions

Chen, Han, Coseno, Molly, Ficarro, Scott B., Mansueto, My Sam, Komazin-Meredith, Gloria, Boissel, Sandrine, Filman, David J., Marto, Jarrod A., Hogle, James M., Coen, Donald M.

Journal:

ACS Infectious Diseases

Year:

2017

Language:

english

File:

PDF, 2.69 MB

english, 2017

49

STK40 Is a Pseudokinase that Binds the E3 Ubiquitin Ligase COP1

Durzynska, Izabela, Xu, Xiang, Adelmant, Guillaume, Ficarro, Scott B., Marto, Jarrod A., Sliz, Piotrek, Uljon, Sacha, Blacklow, Stephen C.

Journal:

Year:

2017

Language:

english

File:

PDF, 2.21 MB

english, 2017

50

Robust Phosphoproteomic Profiling of Tyrosine Phosphorylation Sites from Human T Cells Using Immobilized Metal Affinity Chromatography and Tandem Mass Spectrometry

Brill, Laurence M., Salomon, Arthur R., Ficarro, Scott B., Mukherji, Mridul, Stettler-Gill, Michelle, Peters, Eric C.

Journal:

Analytical Chemistry

Year:

2004

Language:

english

File:

PDF, 166 KB

english, 2004

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