Post alignment clustering procedure for comparative quantitative proteomics LC-MS data.
Comparative LC-MS is a powerful method for detailed quantitative comparison of complex protein mixtures. Dedicated software is required for detection, matching, and alignment of peaks in multiple LC-MS datasets. However, retention time shifts, saturation effects, limitations of experimental accuracy, and possible occurrence of split peaks make it difficult for software to perfectly match all chromatograms. We describe a procedure to assess the above problems and show that dataset quality can be enhanced with the aid of cluster analysis.
de Groot
Joost C W
JC
Plant Research International, Wageningen-UR, Wageningen, The Netherlands.
Fiers
Mark W E J
MW
van Ham
Roeland C H J
RC
America
Antoine H P
AH
D002853:Chromatography, Liquid / Q000706:statistics & numerical data; D016000:Cluster Analysis; D010449:Peptide Mapping / Q000379:methods / Q000706:statistics & numerical data; D010940:Plant Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods / Q000706:statistics & numerical data; D013025:Glycine max / Q000737:chemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods / Q000706:statistics & numerical data
D010940:Plant Proteins