A new protocol of analyzing isotope-coded affinity tag data from high-resolution LC–MS spectrometry

Abstract

Isotope-coded affinity tags (ICAT) is a labeling technique that provides insights into quantitative molecular changes. In this paper, we propose a new protocol to identify and analyze ICAT labeled peak pairs in high-resolution LC-MS data. Our major contributions are: (1) we use isotope distance constraint, ICAT distance constraint, and LC-span constraint to identify ICAT labeled peak pairs and (2) we propose to trigger tandem MS/MS scanning based on the ratio estimation value of identified ICAT peak pairs instead of the peak intensity values. Compared with current approaches that choose peaks with high intensity values for tandem MS/MS scanning, the new protocol can improve the scanning efficiency and accuracy.

Applications of Proteomic Tools to Study Insect Vector–Plant Virus Interactions

“…Labeled proteomic approaches enable the evaluation of a mixture of samples in one run which can later be identified by the presence of a unique label of the samples. Samples are typically labeled with radioisotopes via metabolic labeling, a process feasible only for cell cultures which was soon replaced by chemical modification of specific amino acids in intact proteins, such as an isotope-coded affinity tag [53], isotope-coded protein label [54] and the most advanced being the isobaric tags for relative and absolute quantitation (iTRAQ) [55]. Up to four samples can be compared with the reagents available for iTRAQ.…”