Supporting data for the MS identification of distinct transferrin glycopeptide glycoforms and citrullinated peptides associated with inflammation or autoimmunity.

A Rosal-Vela,E Giménez,V Sanz-Nebot,J Postigo,J Sancho,M Iglesias,R Merino,A Barroso,S García-Rodríguez,J Merino,V Longobardo,A Lario,M Zubiaur

doi:10.1016/j.dib.2015.12.045

Abstract

This data article presents the results of all the statistical analyses applied to the relative intensities of the detected 2D-DiGE protein spots for each of the 3 performed DiGE experiments. The data reveals specific subsets of protein spots with significant differences between WT and CD38-deficient mice with either Collagen-induced arthritis (CIA), or with chronic inflammation induced by CFA, or under steady-state conditions. This article also shows the MS data analyses that allowed the identification of the protein species which serve to discriminate the different experimental groups used in this study. Moreover, the article presents MS data on the citrullinated peptides linked to specific protein species that were generated in CIA+ or CFA-treated mice. Lastly, this data article provides MS data on the efficiency of the analyses of the transferrin (Tf) glycopeptide glycosylation pattern in spleen and serum from CIA+ mice and normal controls. The data supplied in this work is related to the research article entitled “identification of multiple transferrin species in spleen and serum from mice with collagen-induced arthritis which may reflect changes in transferrin glycosylation associated with disease activity: the role of CD38” [1]. All mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with identifiers PRIDE: PXD002644, PRIDE: PXD002643, PRIDE: PXD003183 and PRIDE: PXD003163.

Highlights

This data article presents the results of all the statistical analyses applied to the relative intensities of the detected 2D-DiGE protein spots for each of the 3 performed DiGE experiments
The data reveals specific subsets of protein spots with significant differences between WT and CD38deficient mice with either Collagen-induced arthritis (CIA), or with chronic inflammation induced by CFA, or under steady-state conditions
MS data on the citrullinated peptides linked to specific protein species that were generated in CIA þ or CFA-treated mice

Summary

Data accessibility

Healthcare) using the Differential In-gel Analysis (DIA) module to detect and normalize the protein spots. Protein extracts from mice subjected to different experimental conditions were analyzed by 2D-DiGE, and protein species that differed in abundance were identified by MS/MS. Tf glycopeptide glycoforms detected by mLC–TOF–MS in the spots of spleen protein extracts subjected to 2D electrophoretic separation and in-gel tryptic digestion. Protein spots from mouse spleen identified by MS/MS using the 4800 MALDI-TOF/TOF (AB Sciex). The sequence of matched and fragmented peptides of the identified proteins, plus the ion scores and confidence intervals of the fragmented peptides can be found in the online version of this article (Table 1, .xlsx file) as supplementary material. The sequence of matched and fragmented peptides plus the ion scores and confidence intervals of the fragmented peptides can be found in the online version of this article (Table 2, .xlsx file) as supplementary material.

WT: CD38 KO

Protein extraction from spleen preparations

Design of DiGE experiments

DiGE labeling and two-dimensional gel electrophoresis