PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry.
- B. Ma, Kaizhong Zhang, G. Lajoie
- Biology, Computer ScienceRapid Communications in Mass Spectrometry
- 30 October 2003
A new de novo sequencing software package, PEAKS, is described, to extract amino acid sequence information without the use of databases, using a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum.
PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification*
- Jing Zhang, L. Xin, B. Ma
- Computer ScienceMolecular & Cellular Proteomics
- 20 December 2011
A new database search tool, PEAKS DB, has been developed by incorporating the de novo sequencing results into the database search, and achieves significantly improved accuracy and sensitivity over two other commonly used software packages.
Matrigel: A complex protein mixture required for optimal growth of cell culture
- Chris S Hughes, L. Postovit, G. Lajoie
- BiologyProteomics
- 1 May 2010
The ability to identify the low mass and abundance components of Matrigel illustrates the utility of this method for the analysis of the extracellular matrix, as well as the complexity of the matrix itself.
IGF and FGF cooperatively establish the regulatory stem cell niche of pluripotent human cells in vitro
- S. Bendall, Morag H. Stewart, M. Bhatia
- BiologyNature
- 30 August 2007
This study demonstrates a direct role of the IGF-II/IGF1R axis on human ES cell physiology and establishes that hdFs produced by human ES cells themselves define the stem cell niche of pluripotent human stem cells.
The Drosophila Nuclear Receptor E75 Contains Heme and Is Gas Responsive
- J. Reinking, Mandy M. Lam, H. Krause
- BiologyCell
- 29 July 2005
Characterization of staphyloferrin A biosynthetic and transport mutants in Staphylococcus aureus
- Federico C. Beasley, E. Vinés, D. Heinrichs
- BiologyMolecular Microbiology
- 1 May 2009
It is provided here that HtsABC, along with the FhuC ATPase, is required for the uptake of staphyloferrin A, a polycarboxylate siderophore, and crystal structure of apo‐HtsA was determined and identified a large positively charged region in the substrate‐binding pocket, in agreement with a role in binding of anionic staphylloferrins A.
The Structural Basis of Gas-Responsive Transcription by the Human Nuclear Hormone Receptor REV-ERBβ
- K. Pardee, Xiaohui Xu, A. Edwards
- BiologyPLoS Biology
- 1 February 2009
It is shown that transcription repression mediated by heme-bound REV-ERBs is reversed by the addition of nitric oxide (NO), and that the heme and NO effects are mediated by the C-terminal ligand-binding domain (LBD).
Chitinase genes responsive to cold encode antifreeze proteins in winter cereals.
- S. Yeh, B. Moffatt, G. Lajoie
- BiologyPlant Physiology
- 1 November 2000
It is concluded that two novel cold-responsive genes encoding chitinases with ice-binding activity may have arisen in winter rye and other cereals through gene duplication.
Role of Siderophore Biosynthesis in Virulence of Staphylococcus aureus: Identification and Characterization of Genes Involved in Production of a Siderophore
- Suzanne E. Dale, A. Doherty-Kirby, G. Lajoie, D. Heinrichs
- BiologyInfection and Immunity
- 1 January 2004
It is shown that S. aureus strains RN6390 and Newman produce siderophore when the cells are starved for iron, and a nine-gene, iron-regulated operon is identified and characterized, situated between sirABC and galE on the S.aureus chromosome, that is involved in the production of a siderophile.
PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS
- B. Ma, Kaizhong Zhang, G. Lajoie
- Biology, Computer Science
- 2003
A new de novo sequencing software package, PEAKS, is described, to extract amino acid sequence information without the use of databases, using a new model and a new algorithm to efficiently compute the best peptide sequence whose fragment ions can best interpret the peaks in the MS/MS spectrum.
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