Label-free quantitation, an extension to 2DB.
Determining the differential expression of proteins under different conditions is of major importance in proteomics. Since mass spectrometry-based proteomics is often used to quantify proteins, several labelling strategies have been developed. While these are generally more precise than label-free quantitation approaches, they imply specifically designed experiments which also require knowledge about peptides that are expected to be measured and need to be modified. We recently designed the 2DB database which aids storage, analysis, and publication of data from mass spectrometric experiments to identify proteins. This database can aid identifying peptides which can be used for quantitation. Here an extension to the database application, named MSMAG, is presented which allows for more detailed analysis of the distribution of peptides and their associated proteins over the fractions of an experiment. Furthermore, given several biological samples in the database, label-free quantitation can be performed. Thus, interesting proteins, which may warrant further investigation, can be identified en passant while performing high-throughput proteomics studies.
Allmer
Jens
J
Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey. jens@allmer.de
D003198:Computer Simulation; D057225:Data Mining; D030562:Databases, Protein; D001330:Electronic Data Processing / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D057166:High-Throughput Screening Assays; D010446:Peptide Fragments / Q000032:analysis; D010455:Peptides / Q000032:analysis; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry
D010446:Peptide Fragments; D010455:Peptides; D011506:Proteins