ProtQuant: a tool for the label-free quantification of MudPIT proteomics data.
BACKGROUND
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*, uses "below threshold" peptide scores to provide meaningful non-zero values for missing data points. We demonstrate that SigmaXCorr* produces an average reduction in false positive identifications of differential expression of 25% compared to SigmaXCorr.


CONCLUSIONS
ProtQuant is a tool for protein quantification built for multi-platform use with an intuitive user interface. ProtQuant efficiently and uniquely performs label-free quantification of protein datasets produced with Sequest and provides the user with facilities for data management and analysis. Importantly, ProtQuant is available as a self-installing executable for the Windows environment used by many bench scientists.
Bridges
Susan M
SM
Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA. bridges@cse.msstate.edu
Magee
G Bryce
GB
Wang
Nan
N
Williams
W Paul
WP
Burgess
Shane C
SC
Nanduri
Bindu
B
D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D010449:Peptide Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012106:Research; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D011506:Proteins