The IGBB logo features a stylized "pinwheel" to the left of the letters IGBB in caps in a modified Bank Gothic Pro font.
The six-part "pinwheel" in the IGBB logo is:
- A symbol of lab unity as it shows "parts" coming together to make a "whole."
- A flower or three-leaf clover representing (a) plants, important subjects of our research, (b) life in general, and (c) the life sciences (biology).
- A set of chromosomes being moved towards the center of a cell.
- The Sun - another symbol of life.
- A protein composed of six subunits (e.g., a protein pore).
- Three foxes putting their heads together. The fox is a symbol of cleverness in Western folklore. Since the IGBB is organized into three service groups (Genomics, Proteomics/Metabolomics, and Biocomputing/Computational Biology), the foxes could represent the three disciplines working together.
- A scientist jumping for joy after making an important discovery.
- A windmill, the primary symbol associated with Cervantes' famous character Don Quixote - Like Don Quixote, scientists must be willing to attack 'wicked giants' (e.g., ignorance, racism, sexism, intolerance, use of the term 'science' in the promotion of non-scientific causes), champion worthy causes (e.g., education, intellectual freedom, human rights, environmental responsibility), and remain optimistic in the face of defeat (e.g., most days in the lab). Hopefully, however, the average scientist can accomplish these tasks without becoming delusional (a problem that squashed Quixote's dreams of becoming a plant molecular biologist).
- A DNA double-helix or protein in cross section.
- Antibodies binding to a protein.
- Whatever you want it to be.
Dr. Nisarga K. NarayanaPostdoctoral Associate
GENOMICS
email(662) 617-1858
352 Dorman Hall
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data
IGBB Authors:
Susan M. Bridges, Shane C. Burgess, Bindu NanduriPUBLICATION YEAR:
2007IMPACT FACTOR:
4.249CITATION COUNT:
47Bridges SM, Magee GB, Wang N, Williams WP, Burgess SC, Nanduri B (2007) ProtQuant: a tool for the label-free quantification of MudPIT proteomics data.
BMC Bioinformatics 8(Suppl 7): S24.
DOI:
10.1186/1471-2105-8-S7-S24EID:
2-s2.0-38549091691PMID: 18047724
DOWNLOAD PDFABSTRACTBACKGROUND: Effective and economical methods for quantitative analysis of high throughput mass spectrometry data are essential to meet the goals of directly identifying, characterizing, and quantifying proteins from a particular cell state. Multidimensional Protein Identification Technology (MudPIT) is a common approach used in protein identification. Two types of methods are used to detect differential protein expression in MudPIT experiments: those involving stable isotope labelling and the so-called label-free methods. Label-free methods are based on the relationship between protein abundance and sampling statistics such as peptide count, spectral count, probabilistic peptide identification scores, and sum of peptide Sequest XCorr scores (SigmaXCorr). Although a number of label-free methods for protein quantification have been described in the literature, there are few publicly available tools that implement these methods. We describe ProtQuant, a Java-based tool for label-free protein quantification that uses the previously published SigmaXCorr method for quantification and includes an improved method for handling missing data. RESULTS: ProtQuant was designed for ease of use and portability for the bench scientist. It implements the SigmaXCorr method for label free protein quantification from MudPIT datasets. ProtQuant has a graphical user interface, accepts multiple file formats, is not limited by the size of the input files, and can process any number of replicates and any number of treatments. In addition, ProtQuant implements a new method for dealing with missing values for peptide scores used for quantification. The new algorithm, called SigmaXCorr.
The IGBB is supported, in part, by the following units:
The IGBB is an HPC² member center.
