Proteome identification of the silkworm middle silk gland.

Jian-Ying Li,Bo-Xiong Zhong,Jia-Qian Che,Lu-Peng Ye,Jia Song,Zheng-Ying You,Shao-Hua Wang

doi:10.1016/j.dib.2016.01.053

Jian-Ying Li, Bo-Xiong Zhong + Show 5 more

Open Access

https://doi.org/10.1016/j.dib.2016.01.053

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Journal: Data in Brief	Publication Date: Feb 4, 2016
Citations: 3	License type: cc-by

Affiliation: Hangzhou Normal University, Zhejiang University

Abstract

To investigate the functional differentiation among the anterior (A), middle (M), and posterior (P) regions of silkworm middle silk gland (MSG), their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014) [1] via the PRIDE partner repository (Vizcaino, 2013) [2] with the dataset identifier PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP) after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015) [3].

Highlights

To investigate the functional differentiation among the anterior (A), middle (M), and posterior (P) regions of silkworm middle silk gland (MSG), their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al, 2014) [1] via the PRIDE partner repository (Vizcaino, 2013) [2] with the dataset identifier PXD003371
The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP) after database search with Mascot software were available in .XML format files

Summary

Data accessibility

Excel data sheets with identified proteins and corresponding peptides from each analyzed sample. The sample proteomes were fractionated using 1D SDS-PAGE followed by tryptic digest. Digested peptides were fractionated using MDLC system prior to LC–MS/MS. High-confidence proteome identifications of the silkworm middle silk gland. The identified tissue-specific proteins are valuable for understanding of the functional differentiation among different regions of middle silk gland. Label-free quantitation of the three regions of silkworm middle silk gland to determine their relative abundances. In-depth proteome comparison with posterior silk gland will contribute to better understanding of the mechanism of silk protein synthesis. In order to disclose the mechanism of high efficient synthesis of silk proteins, in-depth proteomic analysis of the silkworm middle silk gland (MSG) was performed with shotgun LC–MS/MS. The digested peptides were analyzed using a Nano-LC–MS/MS system with a LTQ-Orbitrap mass spectrometer. The differentially expressed proteins were further subjected to functional enrichment analysis (Fig. 1)

Sample preparation

Findings

Protein separation and in-gel digestion