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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

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

3

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

4

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

5

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

6

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

7

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

8

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

9

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

10

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

11

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

12

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

13

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

14

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

15

Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites

Scott B. Ficarro, Arthur R. Salomon, Laurence M. Brill, Daniel E. Mason, Michelle Stettler-Gill, Ansgar Brock, Eric C. Peters

Journal:

Rapid Communications in Mass Spectrometry

Year:

2005

Language:

english

File:

PDF, 289 KB

english, 2005

16

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

17

Enrichment and analysis of peptide subsets using fluorous affinity tags and mass spectrometry

Brittain, Scott M, Ficarro, Scott B, Brock, Ansgar, Peters, Eric C

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 585 KB

english, 2005

18

C/EBP and DEK coordinately regulate myeloid differentiation

Koleva, R. I., Ficarro, S. B., Radomska, H. S., Carrasco-Alfonso, M. J., Alberta, J. A., Webber, J. T., Luckey, C. J., Marcucci, G., Tenen, D. G., Marto, J. A.

Journal:

Year:

2012

Language:

english

File:

PDF, 862 KB

english, 2012

19

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

20

Discovery of Potent and Selective Covalent Inhibitors of JNK

Tinghu Zhang, Francisco Inesta-Vaquera, Mario Niepel, Jianming Zhang, Scott B. Ficarro, Thomas Machleidt, Ting Xie, Jarrod A. Marto, NamDoo Kim, Taebo Sim, John D. Laughlin, Hajeung Park, Philip V. Lo

Journal:

Chemistry & Biology

Year:

2012

Language:

english

File:

PDF, 1.31 MB

english, 2012

21

multiplierz: an extensible API based desktop environment for proteomics data analysis

Jignesh R Parikh, Manor Askenazi, Scott B Ficarro, Tanya Cashorali, James T Webber, Nathaniel C Blank, Yi Zhang, Jarrod A Marto

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.80 MB

english, 2009

22

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

23

Phosphoproteomic Analysis of Human Embryonic Stem Cells

Laurence M. Brill, Wen Xiong, Ki-Bum Lee, Scott B. Ficarro, Andrew Crain, Yue Xu, Alexey Terskikh, Evan Y. Snyder, Sheng Ding

Journal:

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

24

Superantigen Disruption of CD8+ T and B lymphocyte Homeostasis

Carlo Rago, Kristina Tocce, Scott Ficarro, Greeg Masters, James Riggs

Journal:

Year:

2000

Language:

english

File:

PDF, 1.69 MB

english, 2000

25

Phosphoproteome Analysis of Capacitated Human Sperm: EVIDENCE OF TYROSINE PHOSPHORYLATION OF A KINASE-ANCHORING PROTEIN 3 AND VALOSIN-CONTAINING PROTEIN/p97 DURING CAPACITATION

Ficarro, S., Chertihin, O., Westbrook, V. A., White, F., Jayes, F., Kalab, P., Marto, J. A., Shabanowitz, J., Herr, J. C., Hunt, D. F., Visconti, P. E.

Journal:

Journal of Biological Chemistry

Year:

2003

Language:

english

File:

PDF, 312 KB

english, 2003

26

Metabolic Signatures Uncover Distinct Targets in Molecular Subsets of Diffuse Large B Cell Lymphoma

Pilar Caro, Amar U. Kishan, Erik Norberg, Illana A. Stanley, Bjoern Chapuy, Scott B. Ficarro, Klaudia Polak, Daniel Tondera, John Gounarides, Hong Yin, Feng Zhou, Michael R. Green, Linfeng Chen, Stefa

Journal:

Year:

2012

Language:

english

File:

PDF, 1.24 MB

english, 2012

27

An Automated Noncontact Deposition Interface for Liquid Chromatography Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Ericson, Christer, Phung, Qui T., Horn, David M., Peters, Eric C., Fitchett, Jonathan R., Ficarro, Scott B., Salomon, Arthur R., Brill, Laurence M., Brock, Ansgar

Journal:

Analytical Chemistry

Year:

2003

Language:

english

File:

PDF, 515 KB

english, 2003

28

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

29

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

30

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

31

Therapeutic Targeting of Oncogenic K-Ras by a Covalent Catalytic Site Inhibitor

Lim, Sang Min, Westover, Kenneth D., Ficarro, Scott B., Harrison, Rane A., Choi, Hwan Geun, Pacold, Michael E., Carrasco, Martin, Hunter, John, Kim, Nam Doo, Xie, Ting, Sim, Taebo, Jänne, Pasi A., Mey

Journal:

Angewandte Chemie International Edition

Year:

2014

Language:

english

File:

PDF, 1.07 MB

english, 2014

32

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

33

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

34

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

35

In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C

Hunter, J. C., Gurbani, D., Ficarro, S. B., Carrasco, M. A., Lim, S. M., Choi, H. G., Xie, T., Marto, J. A., Chen, Z., Gray, N. S., Westover, K. D.

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 1.06 MB

english, 2014

36

Niobium(V) Oxide (Nb 2 O 5 ): Application to Phosphoproteomics

Ficarro, Scott B., Parikh, Jignesh R., Blank, Nathaniel C., Marto, Jarrod A.

Journal:

Analytical Chemistry

Year:

2008

Language:

english

File:

PDF, 2.12 MB

english, 2008

37

cAMP-dependent Tyrosine Phosphorylation of Subunit I Inhibits Cytochrome c Oxidase Activity

Lee, I., Salomon, A. R., Ficarro, S., Mathes, I., Lottspeich, F., Grossman, L. I., Huttemann, M.

Journal:

Journal of Biological Chemistry

Year:

2005

Language:

english

File:

PDF, 1.11 MB

english, 2005

38

Intrinsic Selectivity of Notch 1 for Delta-like 4 Over Delta-like 1

Andrawes, M. B., Xu, X., Liu, H., Ficarro, S. B., Marto, J. A., Aster, J. C., Blacklow, S. C.

Journal:

Journal of Biological Chemistry

Year:

2013

Language:

english

File:

PDF, 3.23 MB

english, 2013

39

Magnetic Bead Processor for Rapid Evaluation and Optimization of Parameters for Phosphopeptide Enrichment

Ficarro, Scott B., Adelmant, Guillaume, Tomar, Maria N., Zhang, Yi, Cheng, Vincent J., Marto, Jarrod A.

Journal:

Analytical Chemistry

Year:

2009

Language:

english

File:

PDF, 4.93 MB

english, 2009

40

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

41

PARP1-Driven Poly-ADP-Ribosylation Regulates BRCA1 Function in Homologous Recombination-Mediated DNA Repair

Hu, Y., Petit, S. A., Ficarro, S. B., Toomire, K. J., Xie, A., Lim, E., Cao, S. A., Park, E., Eck, M. J., Scully, R., Brown, M., Marto, J. A., Livingston, D. M.

Journal:

Cancer Discovery

Year:

2014

Language:

english

File:

PDF, 3.77 MB

english, 2014

42

Online Nanoflow RP−RP-MS Reveals Dynamics of Multicomponent Ku Complex in Response to DNA Damage

Zhou, Feng, Cardoza, Job D., Ficarro, Scott B., Adelmant, Guillaume O., Lazaro, Jean-Bernard, Marto, Jarrod A.

Journal:

Journal of Proteome Research

Year:

2010

Language:

english

File:

PDF, 4.45 MB

english, 2010

43

Online Nanoflow Multidimensional Fractionation for High Efficiency Phosphopeptide Analysis

Ficarro, S. B., Zhang, Y., Carrasco-Alfonso, M. J., Garg, B., Adelmant, G., Webber, J. T., Luckey, C. J., Marto, J. A.

Journal:

Molecular & Cellular Proteomics

Year:

2011

Language:

english

File:

PDF, 2.77 MB

english, 2011

44

Nanoflow Low Pressure High Peak Capacity Single Dimension LC-MS/MS Platform for High-Throughput, In-Depth Analysis of Mammalian Proteomes

Zhou, Feng, Lu, Yu, Ficarro, Scott B., Webber, James T., Marto, Jarrod A.

Journal:

Analytical Chemistry

Year:

2012

Language:

english

File:

PDF, 1.62 MB

english, 2012

45

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

46

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

47

Identification of Kinase Inhibitor Targets in the Lung Cancer Microenvironment by Chemical and Phosphoproteomics

Gridling, M., Ficarro, S. B., Breitwieser, F. P., Song, L., Parapatics, K., Colinge, J., Haura, E. B., Marto, J. A., Superti-Furga, G., Bennett, K. L., Rix, U.

Journal:

Molecular Cancer Therapeutics

Year:

2014

Language:

english

File:

PDF, 962 KB

english, 2014

48

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

49

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

50

Profiling protein function with small molecule microarrays

Winssinger, N., Ficarro, S., Schultz, P. G., Harris, J. L.

Journal:

Proceedings of the National Academy of Sciences

Year:

2002

Language:

english

File:

PDF, 422 KB

english, 2002