Proteomes 2015, 3, 298-327; doi:10.3390/proteomes3030298 OPEN ACCESS proteomes ISSN 2227-7382 www.mdpi.com/journal/proteomes Article Concurrent Label-Free Mass Spectrometric Analysis of Dystrophin Isoform Dp427 and the Myofibrosis Marker Collagen in Crude Extracts from mdx-4cv Skeletal Muscles Sandra Murphy 1, Margit Zweyer 2, Rustam R. Mundegar 2, Michael Henry 3, Paula Meleady 3, Dieter Swandulla 2 and Kay Ohlendieck 1,* 1 Department of Biology, Maynooth University, National University of Ireland, Maynooth Co. Kildare, Ireland; E-Mail:
[email protected] 2 Department of Physiology II, University of Bonn, Bonn D-53115, Germany; E-Mails:
[email protected] (M.Z.);
[email protected] (R.R.M.);
[email protected] (D.S.) 3 National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland; E-Mails:
[email protected] (M.H.);
[email protected] (P.M.) * Author to whom correspondence should be addressed; E-Mail:
[email protected]; Tel.: +353-1-708-3842; Fax: +353-1-708-3845. Academic Editor: Jatin G Burniston Received: 30 June 2015 / Accepted: 3 September 2015 / Published: 16 September 2015 Abstract: The full-length dystrophin protein isoform of 427 kDa (Dp427), the absence of which represents the principal abnormality in X-linked muscular dystrophy, is difficult to identify and characterize by routine proteomic screening approaches of crude tissue extracts. This is probably related to its large molecular size, its close association with the sarcolemmal membrane, and its existence within a heterogeneous glycoprotein complex. Here, we used a careful extraction procedure to isolate the total protein repertoire from normal versus dystrophic mdx-4cv skeletal muscles, in conjunction with label-free mass spectrometry, and successfully identified Dp427 by proteomic means.