Combining Untargeted and Targeted Proteomic Strategies for Discrimination and Quantification of Cashmere Fibers

RESEARCH ARTICLE Combining Untargeted and Targeted Proteomic Strategies for Discrimination and Quantification of Cashmere Fibers Shanshan Li1, Yong Zhang2, Jihua Wang3, Yunfei Yang2, Chen Miao1, Yufeng Guo1, Zhidan Zhang1, Qichen Cao1*, Wenqing Shui1* 1 Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China, 2 College of Life Sciences, Nankai University, Tianjin, 300071, China, 3 Tianjin Textile Engineering Research Institute, Tianjin, 300308, China * (QCC); (WQS) Abstract OPEN ACCESS Citation: Li S, Zhang Y, Wang J, Yang Y, Miao C, Guo Y, et al. (2016) Combining Untargeted and Targeted Proteomic Strategies for Discrimination and Quantification of Cashmere Fibers. PLoS ONE 11(1): e0147044. doi:10.1371/journal.pone.0147044 Editor: Jon M. Jacobs, Pacific Northwest National Laboratory, UNITED STATES Received: September 6, 2015 Accepted: December 28, 2015 Published: January 20, 2016 Copyright: © 2016 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. The MS data been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD003107. Funding: This work was supported by (WQS) the National Natural Science Foundation of China (No. 31401150), http://www.nsfc.gov.cn; (QCC) the National Natural Science Foundation of China (No. 21505151), http://www.nsfc.gov.cn; (WQS) the Key Projects in the Tianjin Science & Technology Pillar Program (No. 14ZCZDSY00062), http://http://www. tstc.gov.cn/. The funders had no role in study design, Cashmere is regarded as a specialty and luxury fiber due to its scarcity and high economic value. For fiber quality assessment, it is technically very challenging to distinguish and quantify the cashmere fiber from yak or wool fibers because of their highly similar physical appearance and substantial protein sequence homology. To address this issue, we propose a workflow combining untargeted and targeted proteomics strategies for selecting, verifying and quantifying biomarkers for cashmere textile authentication. Untargeted proteomic surveys were first applied to identify 174, 157, and 156 proteins from cashmere, wool and yak fibers, respectively. After marker selection at different levels, peptides turned out to afford much higher selectivity than proteins for fiber species discrimination. Subsequently, parallel reaction monitoring (PRM) methods were developed for ten selected peptide markers. The PRM-based targeted analysis of peptide markers enabled accurate determination of fiber species and cashmere percentages in different fiber mixtures. Furthermore, collective use of these peptide makers allowed us to discriminate and quantify cashmere fibers in commercial finished fabrics that have undergone heavy chemical treatments. Cashmere proportion measurement in fabric samples using our proteomic approach was in good agreement with results from traditional light microscopy, yet our method can be more readily standardized to become an objective and robust assay for assessing authenticity of fibers and textiles. We anticipate that the proteomic strategies presented in our study could be further implicated in discovery of quality trait markers for other products containing highly homologous proteomes. Introduction Animal hair fibers, such as cashmere, wool and yak, are an important source of raw materials in today's textile industry. Cashmere is the downy hair produced by goats (Capra hircus). It is one of the finest and softest materials used for manufacturing high quality luxury textiles. The PLOS ONE | DOI:10.1371/journal.pone.0147044 January 20, 2016 1 / 15 Proteomic Strategies for Qual and Quant of Cashmere Fiber Biomarkers data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. price gap between cashmere and wool is quite significant, which can be 30-fold or even higher [1]. Yak is the fine undercoat fiber of Bos grunniens. Although the external fiber morphology of yak is very similar to that of cashmere, the price of yak is only a quarter that of cashmere [2]. Due to the financial interests and the increasing market demand, there is a rising trend of adulteration of cashmere with cheaper fibers, typically wool or yak, in commercial textiles. Even back to the years 1990–2003, more than two-thirds of cashmere samples analyzed were found to be adulterated [3]. For the sustainable development of textile industry, it has become imperative for cashmere producers and commercial trading partners to accurately assess the quality attributes of raw and processed products. Currently employed methods for fiber quality assessment involve optical microscopy and scanning electron microscopy (SEM) which give information on the surface morphology, internal pigmentation and the fine structure of cuticle cells in the fiber at high resolution [4, 5]. These conventional methods are subjective and heavily depend on the skill and expertise of the operator. A large number of fibers have to be manually examined in regard to fiber diameter, crimp, color, staple strength, etc. Even though, distinguishing fine yak hair and brown cashmere is very difficult or even impossible [6]. Furthermore, the time-consuming procedure and high cost of SEM analysis has hampered its application. More recently, several other techniques have been developed to improve the objectivity and accuracy of fiber blend identification, including analysis of the external and internal lipids [7] or DNA [1, 8, 9] in fibers or developing ‘anti-cashmere’ monoclonal antibodies [10]. Nevertheless, these techniques have not been widely pursued because of concerns in method robustness and cost, especially the accuracy of results often affected by chemical treatments of fibers during textile manufacturing [11]. The major components of mammalian hair fibers are complex mixtures of proteins, yet lipids and carbohydrates are also present [12]. Approximately 90% of the fiber substance by weight is contributed by protein constituents including keratin and keratin associated proteins (KAPs) prominently [13]. Proteomic investigation of fiber composition has been mainly focused on human hair and wool fibers [14–17]. A total of 113 proteins within twenty-five keratin and KAP families were identified in human hair fibers [14, 15, 18]. Among them, 70 proteins classified into 19 keratin and KAP families were also found in wool fibers [19]. In addition, recent work from Clerens and Koehn et al. documented 113, 108 and 118 proteins identified in wool fibers respectively [16, 1 (...truncated)