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1

Aminoglycoside antibiotics induce bacterial biofilm formation

Hoffman, Lucas R., D'Argenio, David A., MacCoss, Michael J., Zhang, Zhaoying, Jones, Roger A., Miller, Samuel I.

Journal:

Year:

2005

Language:

english

File:

PDF, 311 KB

english, 2005

2

Isotope Signatures Allow Identification of Chemically Cross-Linked Peptides by Mass Spectrometry: A Novel Method to Determine Interresidue Distances in Protein Structures through Cross-Linking

Zelter, Alex, Hoopmann, Michael R., Vernon, Robert, Baker, David, MacCoss, Michael J., Davis, Trisha N.

Journal:

Journal of Proteome Research

Year:

2010

Language:

english

File:

PDF, 1.98 MB

english, 2010

3

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

Prakash, Amol, Tomazela, Daniela M., Frewen, Barbara, MacLean, Brendan, Merrihew, Gennifer, Peterman, Scott, MacCoss, Michael J.

Journal:

Journal of Proteome Research

Year:

2009

Language:

english

File:

PDF, 2.19 MB

english, 2009

4

Kojak: Efficient Analysis of Chemically Cross-Linked Protein Complexes

Hoopmann, Michael R., Zelter, Alex, Johnson, Richard S., Riffle, Michael, MacCoss, Michael J., Davis, Trisha N., Moritz, Robert L.

Journal:

Journal of Proteome Research

Year:

2015

Language:

english

File:

PDF, 1.46 MB

english, 2015

5

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

Pino, Lindsay K., Searle, Brian C., Bollinger, James G., Nunn, Brook, MacLean, Brendan, MacCoss, Michael J.

Journal:

Mass Spectrometry Reviews

Year:

2017

Language:

english

File:

PDF, 1.71 MB

english, 2017

6

The Interaction Dynamics of Two Potato Leafroll Virus Movement Proteins Affects Their Localization to the Outer Membranes of Mitochondria and Plastids

DeBlasio, Stacy, Xu, Yi, Johnson, Richard, Rebelo, Ana, MacCoss, Michael, Gray, Stewart, Heck, Michelle

Journal:

Year:

2018

Language:

english

File:

PDF, 10.52 MB

english, 2018

7

Initial Guidelines for Manuscripts Employing Data-independent Acquisition Mass Spectrometry for Proteomic Analysis

Chalkley, Robert J., MacCoss, Michael J., Jaffe, Jacob D., Röst, Hannes L.

Journal:

Molecular & Cellular Proteomics

Year:

2019

Language:

english

File:

PDF, 29 KB

english, 2019

8

Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows

Amodei, Dario, Egertson, Jarrett, MacLean, Brendan X., Johnson, Richard, Merrihew, Gennifer E., Keller, Austin, Marsh, Don, Vitek, Olga, Mallick, Parag, MacCoss, Michael J.

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2019

Language:

english

File:

PDF, 1.31 MB

english, 2019

9

Kinetochore-associated Stu2 promotes chromosome biorientation in vivo

Miller, Matthew P., Evans, Rena K., Zelter, Alex, Geyer, Elisabeth A., MacCoss, Michael J., Rice, Luke M., Davis, Trisha N., Asbury, Charles L., Biggins, Sue, Copenhaver, Gregory P.

Journal:

Year:

2019

Language:

english

File:

PDF, 2.40 MB

english, 2019

10

Composition of Caenorhabditis elegans extracellular vesicles suggests roles in metabolism, immunity, and aging

Russell, Joshua C., Kim, Taek-Kyun, Noori, Ayush, Merrihew, Gennifer E., Robbins, Julia E., Golubeva, Alexandra, Wang, Kai, MacCoss, Michael J., Kaeberlein, Matt

Journal:

Year:

2020

File:

PDF, 998 KB

2020

11

Audit logs to enforce document integrity in Skyline and Panorama

Rohde, Tobias, Chupalov, Rita, Shulman, Nicholas, Sharma, Vagisha, Eckels, Josh, Pratt, Brian S, MacCoss, Michael J, MacLean, Brendan X, Luigi Martelli, Pier

Journal:

Year:

2020

File:

PDF, 174 KB

2020

12

Synthesis and biological evaluation of 5R- and 5S-methyl substituted d- and l-configuration 1,3-dioxolane nucleoside analogs

Sanjib Bera, Leila Malik, Balkrishen Bhat, Steven S. Carroll, Renee Hrin, Malcolm MacCoss, Daniel R. McMasters, Michael D. Miller, Greg Moyer, David B. Olsen, William A. Schleif, Joanne E. Tomassini,

Journal:

Bioorganic & Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 405 KB

english, 2004

13

Computational analysis of shotgun proteomics data

Michael J MacCoss

Journal:

Current Opinion in Chemical Biology

Year:

2005

Language:

english

File:

PDF, 162 KB

english, 2005

14

A High Voltage Asymmetric Waveform Generator for FAIMS

Jesse D. Canterbury, James Gladden, Lon Buck, Roy Olund, Michael J. MacCoss

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2010

Language:

english

File:

PDF, 384 KB

english, 2010

15

Identification of ejaculated proteins in the house mouse (Mus domesticus) via isotopic labeling

Matthew D Dean, Geoffrey D Findlay, Michael R Hoopmann, Christine C Wu, Michael J MacCoss, Willie J Swanson, Michael W Nachman

Journal:

Year:

2011

Language:

english

File:

PDF, 581 KB

english, 2011

16

The ABRF Proteomics Research Group Studies: Educational exercises for qualitative and quantitative proteomic analyses

David B. Friedman, Tracy M. Andacht, Maureen K. Bunger, Allis S. Chien, David H. Hawke, Jeroen Krijgsveld, William S. Lane, Kathryn S. Lilley, Michael J. MacCoss, Robert L. Moritz, Robert E. Settlage,

Journal:

Year:

2011

Language:

english

File:

PDF, 741 KB

english, 2011

17

Comparison between procedures using SDS for shotgun proteomic analyses of complex samples

Michael S. Bereman, Jarrett D. Egertson, Michael J. MacCoss

Journal:

Year:

2011

Language:

english

File:

PDF, 381 KB

english, 2011

18

Direct database searching with MALDI-PSD spectra of peptides

Patrick R. Griffin, Michael J. Maccoss, Richard A. Blevins, Jeffrey S. Aaronson, Jimmy K. Eng, John R., Yates Iii

Journal:

Rapid Communications in Mass Spectrometry

Year:

1995

Language:

english

File:

PDF, 745 KB

english, 1995

19

MS1, MS2, and SQT—three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications

W. Hayes McDonald, David L. Tabb, Rovshan G. Sadygov, Michael J. MacCoss, John Venable, Johannes Graumann, Jeff R. Johnson, Daniel Cociorva, John R. Yates III

Journal:

Rapid Communications in Mass Spectrometry

Year:

2004

Language:

english

File:

PDF, 240 KB

english, 2004

20

Functional Diversification and Evolution of Antifreeze Proteins in the Antarctic FishLycodichthys dearborni

Joanna L. Kelley, Jan E. Aagaard, Michael J. MacCoss, Willie J. Swanson

Journal:

Journal of Molecular Evolution

Year:

2010

Language:

english

File:

PDF, 491 KB

english, 2010

21

Comparative proteomics reveals deficiency of SLC9A1 (sodium/hydrogen exchanger NHE1) in β-adducin null red cells

Jason M. Wooden, Greg L. Finney, Eric Rynes, Michael J. MacCoss, Amy J. Lambert, Raymond F. Robledo, Luanne L. Peters, Diana M. Gilligan

Journal:

British Journal of Haematology

Year:

2011

Language:

english

File:

PDF, 287 KB

english, 2011

22

Bindin from a sea star

Susana Patiño, Jan E. Aagaard, Michael J. MacCoss, Willie J. Swanson, Michael W. Hart

Journal:

Evolution & Development

Year:

2009

Language:

english

File:

PDF, 288 KB

english, 2009

23

Molecular architecture and assembly of the DDB1–CUL4A ubiquitin ligase machinery

Angers, Stephane, Li, Ti, Yi, Xianhua, MacCoss, Michael J., Moon, Randall T., Zheng, Ning

Journal:

Year:

2006

Language:

english

File:

PDF, 457 KB

english, 2006

24

A method for the comprehensive proteomic analysis of membrane proteins

Wu, Christine C., MacCoss, Michael J., Howell, Kathryn E., Yates, John R.

Journal:

Nature Biotechnology

Year:

2003

Language:

english

File:

PDF, 1.46 MB

english, 2003

25

The KLHL12–Cullin-3 ubiquitin ligase negatively regulates the Wnt–β-catenin pathway by targeting Dishevelled for degradation

Angers, Stephane, Thorpe, Chris J., Biechele, Travis L., Goldenberg, Seth J., Zheng, Ning, MacCoss, Michael J., Moon, Randall T.

Journal:

Nature Cell Biology

Year:

2006

Language:

english

File:

PDF, 2.77 MB

english, 2006

26

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Käll, Lukas, Canterbury, Jesse D, Weston, Jason, Noble, William Stafford, MacCoss, Michael J

Journal:

Year:

2007

Language:

english

File:

PDF, 199 KB

english, 2007

27

A glutamate-alanine-leucine (EAL) domain protein of Salmonella controls bacterial survival in mice, antioxidant defence and killing of macrophages: role of cyclic diGMP

Katherine B. Hisert, Michael MacCoss, Michael U. Shiloh, K. Heran Darwin, Shaneen Singh, Roger A. Jones, Sabine Ehrt, Zhaoying Zhang, Barbara L. Gaffney, Sheetal Gandotra, David W. Holden, Diana Murra

Journal:

Molecular Microbiology

Year:

2005

Language:

english

File:

PDF, 926 KB

english, 2005

28

Using iRT, a normalized retention time for more targeted measurement of peptides

Claudia Escher, Lukas Reiter, Brendan MacLean, Reto Ossola, Franz Herzog, John Chilton, Michael J. MacCoss, Oliver Rinner

Journal:

Year:

2012

Language:

english

File:

PDF, 2.17 MB

english, 2012

29

The development of selected reaction monitoring methods for targeted proteomics via empirical refinement

Michael S. Bereman, Brendan MacLean, Daniela M. Tomazela, Daniel C. Liebler, Michael J. MacCoss

Journal:

Year:

2012

Language:

english

File:

PDF, 830 KB

english, 2012

30

A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome

Bereman, Michael S., Tomazela, Daniela M., Heins, Hillary S., Simonato, Manuela, Cogo, Paola E., Hamvas, Aaron, Patterson, Bruce W., Cole, F. Sessions, MacCoss, Michael J.

Journal:

Analytical and Bioanalytical Chemistry

Year:

2012

Language:

english

File:

PDF, 439 KB

english, 2012

31

A major deletion in the surfactant protein-B gene causing lethal respiratory distress

Daniel J Wegner, Torbjörn Hertzberg, Hillary B Heins, Göran Elmberger, Michael J MacCoss, Christopher S Carlson, Lawrence M Nogee, F Sessions Cole, Aaron Hamvas

Journal:

Acta Paediatrica

Year:

2007

Language:

english

File:

PDF, 352 KB

english, 2007

32

High-Speed Data Reduction, Feature Detection, and MS/MS Spectrum Quality Assessment of Shotgun Proteomics Data Sets Using High-Resolution Mass Spectrometry

Hoopmann, Michael R., Finney, Gregory L., MacCoss, Michael J.

Journal:

Analytical Chemistry

Year:

2007

Language:

english

File:

PDF, 469 KB

english, 2007

33

RETRACTED: Comparative proteomics reveals deficiency of NHE-1 (Slc9a1) in RBCs from the beta-adducin knockout mouse model of hemolytic anemia

Diana M. Gilligan, Greg L. Finney, Eric Rynes, Michael J. MacCoss, Amy J. Lambert, Luanne L. Peters, Raymond F. Robledo, Jason M. Wooden

Journal:

Blood Cells, Molecules, and Diseases

Year:

2011

Language:

english

File:

PDF, 1.56 MB

english, 2011

34

Retraction notice to “Comparative proteomics reveals deficiency of NHE-1 (Slc9a1) in RBCs from the beta-adducin knockout mouse model of hemolytic anemia” [Blood Cells Mol. Dis. 47 (2011) 85–94]

Diana M. Gilligan, Greg L. Finney, Eric Rynes, Michael J. MacCoss, Amy J. Lambert, Luanne L. Peters, Raymond F. Robledo, Jason M. Wooden

Journal:

Blood Cells, Molecules, and Diseases

Year:

2012

Language:

english

File:

PDF, 92 KB

english, 2012

35

An E3 Ubiquitin Ligase Prevents Ectopic Localization of the Centromeric Histone H3 Variant via the Centromere Targeting Domain

Prerana Ranjitkar, Maximilian O. Press, Xianhua Yi, Richard Baker, Michael J. MacCoss, Sue Biggins

Journal:

Year:

2010

Language:

english

File:

PDF, 1.03 MB

english, 2010

36

Biomarkers of organophosphorus (OP) exposures in humans

Judit Marsillach, Rebecca J. Richter, Jerry H. Kim, Richard C. Stevens, Michael J. MacCoss, Daniela Tomazela, Stephanie M. Suzuki, Lawrence M. Schopfer, Oksana Lockridge, Clement E. Furlong

Journal:

NeuroToxicology

Year:

2011

Language:

english

File:

PDF, 588 KB

english, 2011

37

P188. Structural insights into NOS regulatory mechanisms: What? where? how?

Elsa D. Garcin-Hosfield, Andrew S. Arvai, Robin J. Rosenfeld, Joseph Bonaventura, Mika Aoyagi Scharber, Christopher M. Bruns, David J. Hosfield, S. Jane Lloyd, Michael J. MacCoss, John Yates III, Maur

Journal:

Year:

2006

Language:

english

File:

PDF, 63 KB

english, 2006

38

Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection

Roza Wojcik, Yihan Li, Michael J. MacCoss, Norman J. Dovichi

Journal:

Year:

2012

Language:

english

File:

PDF, 426 KB

english, 2012

39

Effects of Column and Gradient Lengths on Peak Capacity and Peptide Identification in Nanoflow LC-MS/MS of Complex Proteomic Samples

Edward J. Hsieh, Michael S. Bereman, Stanley Durand, Gary A. Valaskovic, Michael J. MacCoss

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2013

Language:

english

File:

PDF, 435 KB

english, 2013

40

De NovoCorrection of Mass Measurement Error in Low Resolution Tandem MS Spectra for Shotgun Proteomics

Jarrett D. Egertson, Jimmy K. Eng, Michael S. Bereman, Edward J. Hsieh, Gennifer E. Merrihew, Michael J. MacCoss

Journal:

Journal of the American Society for Mass Spectrometry

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

41

Characterization of the binding and activity of a high affinity, pseudoirreversible morpholino tachykinin NK1 receptor antagonist

Margaret A Cascieri, Elzbieta Ber, Tung Ming Fong, Jeffrey J Hale, Frank Tang, Lin-Lin Shiao, Sander G Mills, Malcolm MacCoss, Sharon Sadowski, Michael R Tota, Catherine D Strader

Journal:

European Journal of Pharmacology

Year:

1997

Language:

english

File:

PDF, 281 KB

english, 1997

42

Homopteran Vector Biomarkers for Efficient Circulative Plant Virus Transmission are Conserved in Multiple Aphid Species and the Whitefly Bemisia tabaci

Michelle Cilia, Michael Bereman, Tara Fish, Michael J MacCoss, Stewart Gray

Journal:

Journal of Integrative Agriculture

Year:

2012

Language:

english

File:

PDF, 323 KB

english, 2012

43

Comparison of Database Search Strategies for High Precursor Mass Accuracy MS/MS Data

Hsieh, Edward J., Hoopmann, Michael R., MacLean, Brendan, MacCoss, Michael J.

Journal:

Journal of Proteome Research

Year:

2010

Language:

english

File:

PDF, 2.85 MB

english, 2010

44

Probability-Based Validation of Protein Identifications Using a Modified SEQUEST Algorithm

MacCoss, Michael J., Wu, Christine C., Yates, John R.

Journal:

Analytical Chemistry

Year:

2002

Language:

english

File:

PDF, 238 KB

english, 2002

45

Analysis of Peptide MS/MS Spectra from Large-Scale Proteomics Experiments Using Spectrum Libraries

Frewen, Barbara E., Merrihew, Gennifer E., Wu, Christine C., Noble, William Stafford, MacCoss, Michael J.

Journal:

Analytical Chemistry

Year:

2006

Language:

english

File:

PDF, 183 KB

english, 2006

46

Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis

Wu, Christine C., MacCoss, Michael J., Howell, Kathryn E., Matthews, Dwight E., Yates, John R.

Journal:

Analytical Chemistry

Year:

2004

Language:

english

File:

PDF, 131 KB

english, 2004

47

Label-Free Quantitation of Protein Modifications by Pseudo Selected Reaction Monitoring with Internal Reference Peptides

Sherrod, Stacy D., Myers, Matthew V., Li, Ming, Myers, Jeremy S., Carpenter, Kristin L., MacLean, Brendan, MacCoss, Michael J., Liebler, Daniel C., Ham, Amy-Joan L.

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 4.86 MB

english, 2012

48

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

Park, Christopher Y., Klammer, Aaron A., Käll, Lukas, MacCoss, Michael J., Noble, William S.

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 1.13 MB

english, 2008

49

Rapid Assessment of RNAi-mediated Protein Depletion by Selected Reaction Monitoring Mass Spectrometry

Glukhova, Veronika A., Tomazela, Daniela M., Findlay, Geoffrey D., Monnat, Raymond J., MacCoss, Michael J.

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 1.88 MB

english, 2013

50

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

Woo, Sunghee, Cha, Seong Won, Merrihew, Gennifer, He, Yupeng, Castellana, Natalie, Guest, Clark, MacCoss, Michael, Bafna, Vineet

Journal:

Journal of Proteome Research

Year:

2014

Language:

english

File:

PDF, 378 KB

english, 2014