Update information. According to a previous study on the microscopic examination of stem barks in ramie, bast fibers from different parts of stem bark showed distinct differences at the developmental level: specifically, the barks in the top part of stem (TPS) did not initiate fiber growth, whereas barks in the middle part of stem (MPS) had a large number of fibers with thickening secondary walls. We have performed the Ubiquitylome analysis for the tissues of TPS and MPS, and then carried out the comparison of Ubiquitination level of proteins between two tissues, thereby to identified differentially Ubiquitinated proteins. These datasets represent the raw UHPLC spectra for Ubiquitylome of ramie TP S and MPS.