This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The MacCoss lab distributed the following software in 2010-2011: MakeMS2: A windows program for extracting mass spectrometry data from Thermo Fisher RAW instrument files. Hardklor /Kronik: A pair of programs for the analysis of high resolution mass spectrometry data. Hardklor will return monoisotopic m/z and charge states for single or overlapping peptide/protein isotope distributions. CRAWDAD: A software suite for label-free relative quantitation of high- and low-resolution LC-MS data. Replicate runs are aligned in the retention time dimension prior to feature detection using dynamic time warping. Features of differential intensity are detected using statistical tests, and annotated using MS/MS peptide identifications. MScout: A software tool for assessing LC-MS data quality. P3 Predictor: A simple windows program to aide in establishing SRM transitions for targeted proteomics. IDCalc: A Microsoft Windows program that implements the method reported by Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119 for the prediction of isotope distributions. Skyline: A Windows client application for building Selected Reaction Monitoring methods and analyzing the resulting mass spectrometry data. PAnDA: PAnDA is an acronym for Post Analysis Data Acquisition. PAnDA uses the Hardklor feature finder to determine the molecular species in an LC-MS analysis and then uses this information to automatically construct new methods to acquire features missed in prior analyses. Topograph: A Microsoft Windows application for the analysis of mass spectrometry data from biological samples that have been labeled with stable isotope labeled amino acid(s) BullsEye: A program for correcting the monoisotopic m/z for MS/MS spectra from hybrid LTQ-FT and LTQ-Orbitrap mass spectrometers. PepLynx: A program for the interpretation of high resolution MS/MS spectra of cross-linked peptides. P3 Predictor: A simple windows program to aide in establishing SRM transitions for targeted proteomics.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
2P41RR011823-16
Application #
8365838
Study Section
Special Emphasis Panel (ZRG1-CB-L (40))
Project Start
2011-09-01
Project End
2012-06-30
Budget Start
2011-09-01
Budget End
2012-06-30
Support Year
16
Fiscal Year
2011
Total Cost
$9,940
Indirect Cost
Name
University of Washington
Department
Biochemistry
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Luhtala, Natalie; Aslanian, Aaron; Yates 3rd, John R et al. (2017) Secreted Glioblastoma Nanovesicles Contain Intracellular Signaling Proteins and Active Ras Incorporated in a Farnesylation-dependent Manner. J Biol Chem 292:611-628
Ogami, Koichi; Richard, Patricia; Chen, Yaqiong et al. (2017) An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression. Genes Dev :
Ju Lee, Hyun; Bartsch, Deniz; Xiao, Cally et al. (2017) A post-transcriptional program coordinated by CSDE1 prevents intrinsic neural differentiation of human embryonic stem cells. Nat Commun 8:1456
Thakar, Sonal; Wang, Liqing; Yu, Ting et al. (2017) Evidence for opposing roles of Celsr3 and Vangl2 in glutamatergic synapse formation. Proc Natl Acad Sci U S A 114:E610-E618
Jin, Meiyan; Fuller, Gregory G; Han, Ting et al. (2017) Glycolytic Enzymes Coalesce in G Bodies under Hypoxic Stress. Cell Rep 20:895-908
Di Maggio, Lucía Sánchez; Tirloni, Lucas; Pinto, Antonio F M et al. (2016) Across intra-mammalian stages of the liver f?luke Fasciola hepatica: a proteomic study. Sci Rep 6:32796
Wang, Jiyong; Cohen, Allison L; Letian, Anudari et al. (2016) The proper connection between shelterin components is required for telomeric heterochromatin assembly. Genes Dev 30:827-39
Shan, Chun-Min; Wang, Jiyong; Xu, Ke et al. (2016) A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Elife 5:
Kim, Tae Kwon; Tirloni, Lucas; Pinto, Antônio F M et al. (2016) Ixodes scapularis Tick Saliva Proteins Sequentially Secreted Every 24 h during Blood Feeding. PLoS Negl Trop Dis 10:e0004323
Silva, Erica; Betleja, Ewelina; John, Emily et al. (2016) Ccdc11 is a novel centriolar satellite protein essential for ciliogenesis and establishment of left-right asymmetry. Mol Biol Cell 27:48-63

Showing the most recent 10 out of 578 publications