Table of Contents Author Guidelines Submit a Manuscript
Journal of Biomedicine and Biotechnology
Volume 2010, Article ID 840518, 6 pages
http://dx.doi.org/10.1155/2010/840518
Review Article

Mass Spectrometry-Based Label-Free Quantitative Proteomics

1Center on Proteolytic Pathways, Burnham Institute for Medical Research, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
2Department of Dermatology, University of California, San Diego, CA 92093, USA

Received 1 July 2009; Accepted 1 September 2009

Academic Editor: Pieter C. Dorrestein

Copyright © 2010 Wenhong Zhu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citations to this Article [320 citations]

The following is the list of published articles that have cited the current article.

  • Carmen D. Tekwe, Alan R. Dabney, and Raymond J. Carroll, “Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data,” 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), pp. 97–100, . View at Publisher · View at Google Scholar
  • Saloni Walia, Allen C. Clermont, Ben-Bo Gao, Lloyd Paul Aiello, and Edward P. Feener, “Vitreous Proteomics and Diabetic Retinopathy,” Seminars in Ophthalmology, vol. 25, no. 5-6, pp. 289–294, 2010. View at Publisher · View at Google Scholar
  • Morgan O'Hayre, Catherina L. Salanga, Thomas J. Kipps, Davorka Messmer, Pieter C. Dorrestein, and Tracy M. Handel, “Elucidating the CXCL12/CXCR4 Signaling Network in Chronic Lymphocytic Leukemia through Phosphoproteomics Analysis,” Plos One, vol. 5, no. 7, 2010. View at Publisher · View at Google Scholar
  • N. L. Heinecke, B. S. Pratt, T. Vaisar, and L. Becker, “PepC: proteomics software for identifying differentially expressed proteins based on spectral counting,” Bioinformatics, vol. 26, no. 12, pp. 1574–1575, 2010. View at Publisher · View at Google Scholar
  • Massimiliano Paci, Cristian Rapicetta, and Sally Maramotti, “New biomarkers for lung cancer,” Expert Opinion on Medical Diagnostics, vol. 4, no. 3, pp. 201–224, 2010. View at Publisher · View at Google Scholar
  • Deepa Balasubramaniam, Christie L. Eissler, Cynthia V. Stauffacher, and Mark C. Hall, “Use of selected reaction monitoring data for label-free quantification of protein modification stoichiometry,” Proteomics, vol. 10, no. 23, pp. 4301–4305, 2010. View at Publisher · View at Google Scholar
  • Laurent Gatto, Juan Antonio Vizcaíno, Henning Hermjakob, Wolfgang Huber, and Kathryn S. Lilley, “Organelle proteomics experimental designs and analysis,” Proteomics, vol. 10, no. 22, pp. 3957–3969, 2010. View at Publisher · View at Google Scholar
  • Richard R. Sprenger, and Ole N. Jensen, “Proteomics and the dynamic plasma membrane: Quo Vadis?,” Proteomics, vol. 10, no. 22, pp. 3997–4011, 2010. View at Publisher · View at Google Scholar
  • Holger Husi, Fiona McAllister, Nicos Angelopoulos, Victoria J. Butler, Kevin R. Bailey, Kirk Malone, Logan MacKay, Paul Taylor, Antony P. Page, Nicholas J. Turner, Perdita E. Barran, and Malcolm Walkinshaw, “Selective Chemical Intervention in the Proteome of Caenorhabditis elegans,” Journal of Proteome Research, vol. 9, no. 11, pp. 6060–6070, 2010. View at Publisher · View at Google Scholar
  • Dong-Gi Lee, Norma L. Houston, Severin E. Stevenson, Gregory S. Ladics, Scott McClain, Laura Privalle, and Jay J. Thelen, “Mass spectrometry analysis of soybean seed proteins: optimization of gel-free quantitative workflow,” Analytical Methods, vol. 2, no. 10, pp. 1577–1583, 2010. View at Publisher · View at Google Scholar
  • Maria Gomez-Lazaro, Cornelia Rinn, Miguel Aroso, Francisco Amado, and Michael Schrader, “Proteomic analysis of zymogen granules,” Expert Review of Proteomics, vol. 7, no. 5, pp. 735–747, 2010. View at Publisher · View at Google Scholar
  • Zhenyu Cheng, Owen Z. Woody, Bernard R. Glick, and Brendan J. McConkey, “Characterization of plant-bacterial interactions using proteomic approaches,” Current Proteomics, vol. 7, no. 4, pp. 244–257, 2010. View at Publisher · View at Google Scholar
  • Qingbo Li, “Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates,” International Journal of Proteomics, vol. 2010, pp. 1–15, 2010. View at Publisher · View at Google Scholar
  • Stephanie Byrum, Nathan L. Avaritt, Samuel G. Mackintosh, Josie M. Munkberg, Brian D. Badgwell, Wang L. Cheung, and Alan J. Tackett, “A quantitative proteomic analysis of FFPE melanoma,” Journal of Cutaneous Pathology, vol. 38, no. 11, pp. 933–936, 2011. View at Publisher · View at Google Scholar
  • Ye Lu, Cheng-Zhao Lin, Heng Hu, Jian Mei, Jie Wu, and Xin Shen, “Comparison of the sub-cellular proteome of Mycobacterium tuberculosis isoniazid susceptible strain with resistant strain,” Chinese Journal of Microbiology and Immunology (China), vol. 31, no. 8, pp. 713–717, 2011. View at Publisher · View at Google Scholar
  • Yohei Nanjo, Mohammad-Zaman Nouri, and Setsuko Komatsu, “Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary,” Phytochemistry, vol. 72, no. 10, pp. 1263–1272, 2011. View at Publisher · View at Google Scholar
  • David C. Trudgian, Gabriela Ridlova, Roman Fischer, Mukram M. Mackeen, Nicola Ternette, Oreste Acuto, Benedikt M. Kessler, and Benjamin Thomas, “Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline,” Proteomics, vol. 11, no. 14, pp. 2790–2797, 2011. View at Publisher · View at Google Scholar
  • W Zhang Wei, Jy Zhang Ji-Yang, H Liu Hui, Hc Sun Han-Chang, Cm Xu Chang-Ming, Hb Ma Hai-Bin, Yp Zhu Yun-Ping, and Hw Xie Hong-Wei, “Development of Algorithms for Mass Spectrometry-based Label-free Quantitative Proteomics,” Progress In Biochemistry And Biophysics, vol. 38, no. 6, pp. 506–518, 2011. View at Publisher · View at Google Scholar
  • M. Graos, A. S. T. Lourenco, C. B. Duarte, and I. Baldeiras, “Proteomics-Based Technologies in the Discovery of Biomarkers for Multiple Sclerosis in the Cerebrospinal Fluid,” Current Molecular Medicine, vol. 11, no. 4, pp. 326–349, 2011. View at Publisher · View at Google Scholar
  • Erik J. Soderblom, Melanie Philipp, J. Will Thompson, Marc G. Caron, and M. Arthur Moseley, “Quantitative Label-Free Phosphoproteomics Strategy for Multifaceted Experimental Designs,” Analytical Chemistry, vol. 83, no. 10, pp. 3758–3764, 2011. View at Publisher · View at Google Scholar
  • Na Yang, Shun Feng, Kerby Shedden, Xiaolei Xie, Yashu Liu, Charles J. Rosser, David M. Lubman, and Steven Goodison, “Urinary Glycoprotein Biomarker Discovery for Bladder Cancer Detection Using LC/MS-MS and Label-Free Quantification,” Clinical Cancer Research, vol. 17, no. 10, pp. 3349–3359, 2011. View at Publisher · View at Google Scholar
  • Magnus Berle, Ann C. Kroksveen, Øystein A. Haaland, Thin T. Aye, Jill A. Opsahl, Eystein Oveland, Knut Wester, Rune J. Ulvik, Christian A. Helland, and Frode S. Berven, “Protein profiling reveals inter-individual protein homogeneity of arachnoid cyst fluid and high qualitative similarity to cerebrospinal fluid,” Fluids and Barriers of the CNS, vol. 8, no. 1, 2011. View at Publisher · View at Google Scholar
  • Hercules Moura, Rebecca R. Terilli, Adrian R. Woolfitt, Maribel Gallegos-Candela, Lisa G. McWilliams, Maria I. Solano, James L. Pirkle, and John R. Barr, “Studies on botulinum neurotoxins type/C1 and mosaic/DC using Endopep-MS and proteomics,” Fems Immunology And Medical Microbiology, vol. 61, no. 3, pp. 288–300, 2011. View at Publisher · View at Google Scholar
  • Brendan D. Stamper, Isaac Mohar, Terrance J. Kavanagh, and Sidney D. Nelson, “Proteomic Analysis of Acetaminophen-Induced Changes in Mitochondrial Protein Expression Using Spectral Counting,” Chemical Research In Toxicology, vol. 24, no. 4, pp. 549–558, 2011. View at Publisher · View at Google Scholar
  • A.C. Kroksveen, J.A. Opsahl, T.T. Aye, R.J. Ulvik, and F.S. Berven, “Proteomics of human cerebrospinal fluid: Discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics,” Journal of Proteomics, vol. 74, no. 4, pp. 371–388, 2011. View at Publisher · View at Google Scholar
  • Tara K. Sigdel, Sangho Lee, and Minnie M. Sarwal, “Profiling the proteome in renal transplantation,” PROTEOMICS - Clinical Applications, vol. 5, no. 5-6, pp. 269–280, 2011. View at Publisher · View at Google Scholar
  • Kazuya Wada, Atsushi Ogiwara, Keiko Nagasaka, Naoki Tanaka, and Yasuhiko Komatsu, “i-RUBY: A novel software for quantitative analysis of highly accurate shotgun-proteomics liquid chromatography/tandem mass spectrometry data obtained without stable-isotope labeling of proteins,” Rapid Communications In Mass Spectrometry, vol. 25, no. 7, pp. 960–968, 2011. View at Publisher · View at Google Scholar
  • Gregory E. Rice, “Proteomics and the Placenta,” The Placenta, pp. 197–206, 2011. View at Publisher · View at Google Scholar
  • Jason D. Russell, Ryan T. Hilger, Daniel T. Ladror, Mark A. Tervo, Mark Scalf, Michael R. Shortreed, Joshua J. Coon, and Lloyd M. Smith, “Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis,” Analytical Chemistry, vol. 83, no. 6, pp. 2187–2193, 2011. View at Publisher · View at Google Scholar
  • Kuo-Hsun Chiu, Ying-Hwa Chang, Yu-Shun Wu, Shu-Hui Lee, and Pao-Chi Liao, “Quantitative Secretome Analysis Reveals that COL6A1 is a Metastasis-Associated Protein Using Stacking Gel-Aided Purification Combined with iTRAQ Labeling,” Journal Of Proteome Research, vol. 10, no. 3, pp. 1110–1125, 2011. View at Publisher · View at Google Scholar
  • Lynn A. Beer, Hsin-Yao Tang, Sira Sriswasdi, Kurt T. Barnhart, and David W. Speicher, “Systematic Discovery of Ectopic Pregnancy Serum Biomarkers Using 3-D Protein Profiling Coupled with Label-free Quantitation,” Journal Of Proteome Research, vol. 10, no. 3, pp. 1126–1138, 2011. View at Publisher · View at Google Scholar
  • W. Andrew Lancaster, Jeremy L. Praissman, Farris L. Poole, Aleksandar Cvetkovic, Angeli Lal Menon, Joseph W. Scott, Francis E. Jenney, Michael P. Thorgersen, Ewa Kalisiak, Junefredo V. Apon, Sunia A. Trauger, Gary Siuzdak, John A. Tainer, and Michael W. W. Adams, “A Computational Framework for Proteome-Wide Pursuit and Prediction of Metalloproteins using ICP-MS and MS/MS Data,” Bmc Bioinformatics, vol. 12, 2011. View at Publisher · View at Google Scholar
  • Kay Ohlendieck, “Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques,” Skeletal Muscle, vol. 1, no. 1, 2011. View at Publisher · View at Google Scholar
  • Damian Fermin, Venkatesha Basrur, Anastasia K. Yocum, and Alexey I. Nesvizhskii, “Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis,” Proteomics, vol. 11, no. 7, pp. 1340–1345, 2011. View at Publisher · View at Google Scholar
  • Laetitia Theron, Xavier Fernandez, Nathalie Marty-Gasset, Carole Pichereaux, Michel Rossignol, Christophe Chambon, Didier Viala, Thierry Astruc, and Caroline Molette, “Identification by Proteomic Analysis of Early Post-mortem Markers Involved in the Variability in Fat Loss during Cooking of Mule Duck “Foie Gras”,” Journal of Agricultural and Food Chemistry, vol. 59, no. 23, pp. 12617–12628, 2011. View at Publisher · View at Google Scholar
  • Christie L. Eissler, Steven C. Bremmer, Juan S. Martinez, Laurie L. Parker, Harry Charbonneau, and Mark C. Hall, “A general strategy for studying multisite protein phosphorylation using label-free selected reaction monitoring mass spectrometry,” Analytical Biochemistry, vol. 418, no. 2, pp. 267–275, 2011. View at Publisher · View at Google Scholar
  • Hyunwoo Choi, Sungjoon Lee, Chang-Duk Jun, and Zee-Yong Park, “Development of an off-line capillary column IMAC phosphopeptide enrichment method for label-free phosphorylation relative quantification,” Journal Of Chromatography B-Analytical Technologies In The Biomedical And L, vol. 879, no. 28, pp. 2991–2997, 2011. View at Publisher · View at Google Scholar
  • Lisa M. Jones, Justin B. Sperry, James A. Carroll, and Michael L. Gross, “Fast Photochemical Oxidation of Proteins for Epitope Mapping,” Analytical Chemistry, vol. 83, no. 20, pp. 7657–7661, 2011. View at Publisher · View at Google Scholar
  • Peng-Yu Yang, Kai Liu, Chongjing Zhang, Grace Y. J. Chen, Yuan Shen, Mun Hong Ngai, Martin J. Lear, and Shao Q. Yao, “Chemical Modification and Organelle-Specific Localization of Orlistat-Like Natural-Product-Based Probes,” Chemistry-An Asian Journal, vol. 6, no. 10, pp. 2762–2775, 2011. View at Publisher · View at Google Scholar
  • Haibin Shi, Mahesh Uttamchandani, and Shao Q. Yao, “Applying small molecule microarrays and resulting affinity probe cocktails for proteome profiling of mammalian cell lysates,” Chemistry - An Asian Journal, vol. 6, no. 10, pp. 2803–2815, 2011. View at Publisher · View at Google Scholar
  • Xianyin Lai, Lianshui Wang, Haixu Tang, and Frank A. Witzmann, “A Novel Alignment Method and Multiple Filters for Exclusion of Unqualified Peptides To Enhance Label-Free Quantification Using Peptide Intensity in LC-MS/MS,” Journal Of Proteome Research, vol. 10, no. 10, pp. 4799–4812, 2011. View at Publisher · View at Google Scholar
  • Shalini Makawita, Chris Smith, Ihor Batruch, Yingye Zheng, Felix Rueckert, Robert Gruetzmann, Christian Pilarsky, Steven Gallinger, and Eleftherios P. Diamandis, “Integrated Proteomic Profiling of Cell Line Conditioned Media and Pancreatic Juice for the Identification of Pancreatic Cancer Biomarkers,” Molecular & Cellular Proteomics, vol. 10, no. 10, 2011. View at Publisher · View at Google Scholar
  • Hisham Ben Hamidane, Aleksey Vorobyev, and Yury O. Tsybin, “Repeatability and reproducibility of product ion abundances in electron capture dissociation mass spectrometry of peptides,” European Journal Of Mass Spectrometry, vol. 17, no. 4, pp. 321–331, 2011. View at Publisher · View at Google Scholar
  • Karlie A. Neilson, Naveid A. Ali, Sridevi Muralidharan, Mehdi Mirzaei, Michael Mariani, Gariné Assadourian, Albert Lee, Steven C. van Sluyter, and Paul A. Haynes, “Less label, more free: Approaches in label-free quantitative mass spectrometry,” Proteomics, vol. 11, no. 4, pp. 535–553, 2011. View at Publisher · View at Google Scholar
  • Ching-Seng Ang, Jason Phung, and Edouard C. Nice, “The discovery and validation of colorectal cancer biomarkers,” Biomedical Chromatography, vol. 25, no. 1-2, pp. 82–99, 2011. View at Publisher · View at Google Scholar
  • Christin Christin, Rainer Bischoff, and Péter Horvatovich, “Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC–MS for biomarker discovery,” Talanta, vol. 83, no. 4, pp. 1209–1224, 2011. View at Publisher · View at Google Scholar
  • Heidi Rosenqvist, Juanying Ye, and Ole N. Jensen, “Analytical strategies in mass spectrometry-based phosphoproteomics,” Methods in Molecular Biology, vol. 753, pp. 183–213, 2011. View at Publisher · View at Google Scholar
  • Dagmar Hajkova, Sekhar Rao, and Masaru Miyagi, “Recent technological developments in proteolytic 18O labeling,” Current Proteomics, vol. 8, no. 1, pp. 39–46, 2011. View at Publisher · View at Google Scholar
  • Elham Schokraie, Martina Schnölzer, Uwe Warnken, Agnes Hotz-Wagenblatt, Markus A. Grohme, Steffen Hengherr, Frank Förster, Ralph O. Schill, Marcus Frohme, and Thomas Dandekar, “Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state,” PLoS ONE, vol. 7, no. 9, 2012. View at Publisher · View at Google Scholar
  • Na-Young Han, Eun Hee Kim, Joon Choi, Hookeun Lee, and Ki-Baik Hahm, “Quantitative proteomic approaches in biomarker discovery of inflammatory bowel disease,” Journal of Digestive Diseases, vol. 13, no. 10, pp. 497–503, 2012. View at Publisher · View at Google Scholar
  • Salvatore Cappadona, Peter R. Baker, Pedro R. Cutillas, Albert J. R. Heck, and Bas van Breukelen, “Current challenges in software solutions for mass spectrometry-based quantitative proteomics,” Amino Acids, vol. 43, no. 3, pp. 1087–1108, 2012. View at Publisher · View at Google Scholar
  • L. Arike, K. Valgepea, L. Peil, R. Nahku, K. Adamberg, and R. Vilu, “Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli,” Journal of Proteomics, vol. 75, no. 17, pp. 5437–5448, 2012. View at Publisher · View at Google Scholar
  • Xiulan Chen, Shasha Wei, and Fuquan Yang, “Mitochondria in the pathogenesis of diabetes: A proteomic view,” Protein and Cell, vol. 3, no. 9, pp. 648–660, 2012. View at Publisher · View at Google Scholar
  • Suraj Saraswat, Bruce Snyder, and Dragan Isailovic, “Quantification of HPLC-separated peptides and proteins by spectrofluorimetric detection of native fluorescence and mass spectrometry,” Journal Of Chromatography B-Analytical Technologies In The Biomedical And L, vol. 902, pp. 70–77, 2012. View at Publisher · View at Google Scholar
  • Carmen D. Tekwe, Raymond J. Carroll, and Alan R. Dabney, “Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data,” Bioinformatics, vol. 28, no. 15, pp. 1998–2003, 2012. View at Publisher · View at Google Scholar
  • Iain C. Clark, Hans K. Carlson, Anthony T. Iavarone, and John D. Coates, “Bioelectrical redox cycling of anthraquinone-2,6-disulfonate coupled to perchlorate reduction,” Energy & Environmental Science, vol. 5, no. 7, pp. 7970–7978, 2012. View at Publisher · View at Google Scholar
  • Kai Hou, Huabin Su, Zhiyong Huang, Di Wu, Xiangmei Chen, Liyuan Wang, Quan Hong, Yang Lv, Zhe Feng, Xueguang Zhang, Lingling Wu, and Shaoyuan Cui, “Autophagy can repair endoplasmic reticulum stress damage of the passive Heymann nephritis model as revealed by proteomics analysis,” Journal of Proteomics, vol. 75, no. 13, pp. 3866–3876, 2012. View at Publisher · View at Google Scholar
  • Nuno Carinhas, Rui Oliveira, Paula Marques Alves, Manuel J.T. Carrondo, and Ana P. Teixeira, “Systems biotechnology of animal cells: the road to prediction,” Trends in Biotechnology, vol. 30, no. 7, pp. 377–385, 2012. View at Publisher · View at Google Scholar
  • Robert Cunningham, Di Ma, and Lingjun Li, “Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery,” Frontiers in Biology, vol. 7, no. 4, pp. 313–335, 2012. View at Publisher · View at Google Scholar
  • Sevnur Serim, Ute Haedke, and Steven H. L. Verhelst, “Activity-Based Probes for the Study of Proteases: Recent Advances and Developments,” Chemmedchem, vol. 7, no. 7, pp. 1146–1159, 2012. View at Publisher · View at Google Scholar
  • Floriane Pailleux, and Francis Beaudry, “Internal standard strategies for relative and absolute quantitation of peptides in biological matrices by liquid chromatography tandem mass spectrometry,” Biomedical Chromatography, 2012. View at Publisher · View at Google Scholar
  • Takashi Kubota, David A. Stead, Shin-ichiro Hiraga, Sara ten Have, and Anne D. Donaldson, “Quantitative proteomic analysis of yeast DNA replication proteins,” Methods, vol. 57, no. 2, pp. 196–202, 2012. View at Publisher · View at Google Scholar
  • Qi Wu, Huiming Yuan, Lihua Zhang, and Yukui Zhang, “Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: From qualitative to quantitative analysis-A review,” Analytica Chimica Acta, vol. 731, pp. 1–10, 2012. View at Publisher · View at Google Scholar
  • Yongjin Park, and Joel S. Bader, “How networks change with time,” Bioinformatics, vol. 28, no. 12, pp. I40–I48, 2012. View at Publisher · View at Google Scholar
  • Rebecca L. Roston, Jinpeng Gao, Monika W. Murcha, James Whelan, and Christoph Benning, “TGD1,-2, and-3 Proteins Involved in Lipid Trafficking Form ATP-binding Cassette (ABC) Transporter with Multiple Substrate-binding Proteins,” Journal Of Biological Chemistry, vol. 287, no. 25, pp. 21406–21415, 2012. View at Publisher · View at Google Scholar
  • Jennifer Maselli, Barbara F. Hales, Peter Chan, and Bernard Robaire, “Exposure to Bleomycin, Etoposide, and Cis-Platinum Alters Rat Sperm Chromatin Integrity and Sperm Head Protein Profile,” Biology Of Reproduction, vol. 86, no. 5, 2012. View at Publisher · View at Google Scholar
  • Navin Rauniyar, and Laszlo Prokai, “Mass Spectrometry-Based Methods to Investigate Posttranslational Protein Modifications by Lipid Peroxidation Products,” Mass Spectrometry Handbook, pp. 23–40, 2012. View at Publisher · View at Google Scholar
  • Geraldine Delbes, Akiko Yanagiya, Nahum Sonenberg, and Bernard Robaire, “PABP Interacting Protein 2A (PAIP2A) Regulates Specific Key Proteins During Spermiogenesis in the Mouse,” Biology Of Reproduction, vol. 86, no. 3, 2012. View at Publisher · View at Google Scholar
  • Pamela S. Hair, Charlene G. Echague, Reuben D. Rohn, Neel K. Krishna, Julius O. Nyalwidhe, and Kenji M. Cunnion, “Hyperglycemic conditions inhibit C3-mediated immunologic control of Staphylococcus aureus,” Journal Of Translational Medicine, vol. 10, 2012. View at Publisher · View at Google Scholar
  • Shufang Liang, Zhizhong Xu, Xuejiao Xu, Xia Zhao, Canhua Huang, and Yuquan Wei, “Quantitative proteomics for cancer biomarker discovery,” Combinatorial Chemistry and High Throughput Screening, vol. 15, no. 3, pp. 221–231, 2012. View at Publisher · View at Google Scholar
  • Merry L. Lindsey, Susan T. Weintraub, and Richard A. Lange, “Using extracellular matrix proteomics to understand left ventricular remodeling,” Circulation: Cardiovascular Genetics, vol. 5, no. 1, pp. -o7, 2012. View at Publisher · View at Google Scholar
  • Amelie S. Benk, and Christoph Roesli, “Label-free quantification using MALDI mass spectrometry: considerations and perspectives,” Analytical and Bioanalytical Chemistry, vol. 404, no. 4, pp. 1039–1056, 2012. View at Publisher · View at Google Scholar
  • Ana Sevilla, Benjamin Trinite, and Ihor R. Lemischkapp. 119–137, 2012. View at Publisher · View at Google Scholar
  • Noelia Dasilva, Paula Diez, Sergio Matarraz, Maria Gonzalez-Gonzalez, Sara Paradinas, Alberto Orfao, and Manuel Fuentes, “Biomarker Discovery by Novel Sensors Based on Nanoproteomics Approaches,” Sensors, vol. 12, no. 2, pp. 2284–2308, 2012. View at Publisher · View at Google Scholar
  • Botond Penke, Aniko M. Toth, Istvan Foeldi, Maria Szucs, and Tamas Janaky, “Intraneuronal ss-amyloid and its interactions with proteins and subcellular organelles,” Electrophoresis, vol. 33, no. 24, pp. 3608–3616, 2012. View at Publisher · View at Google Scholar
  • Xiaowen Hou, Fang Xie, and Jonathan V. Sweedler, “Relative Quantitation of Neuropeptides over a Thousand-fold Concentration Range,” Journal Of The American Society For Mass Spectrometry, vol. 23, no. 12, pp. 2083–2093, 2012. View at Publisher · View at Google Scholar
  • Cezary Smaczniak, Na Li, Sjef Boeren, Twan America, Walter van Dongen, Soenita S. Goerdayal, Sacco de Vries, Gerco C. Angenent, and Kerstin Kaufmann, “Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues,” Nature Protocols, vol. 7, no. 12, pp. 2144–2158, 2012. View at Publisher · View at Google Scholar
  • Cezary Smaczniak, Na Li, Sjef Boeren, Twan America, Walter Van Dongen, Soenita S. Goerdayal, Sacco De Vries, Gerco C. Angenent, and Kerstin Kaufmann, “Proteomics-based identification of low-abundance signaling and regulatory protein complexes in native plant tissues,” Nature Protocols, vol. 7, no. 12, pp. 2144–2158, 2012. View at Publisher · View at Google Scholar
  • Josué Pérez-Santiago, Rebeca Diez-Alarcia, Luis F. Callado, Jin X. Zhang, Gursharan Chana, Cory H. White, Stephen J. Glatt, Ming T. Tsuang, Ian P. Everall, J. Javier Meana, and Christopher H. Woelk, “A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia,” Journal of Psychiatric Research, vol. 46, no. 11, pp. 1464–1474, 2012. View at Publisher · View at Google Scholar
  • C Chang Cheng, Sf Wu Song-Feng, J Ma Jie, W Zhang Wei, and Yp Zhu Yun-Ping, “Methods and Progress of Mass Spectrometry-based Selected Reaction Monitoring,” Progress In Biochemistry And Biophysics, vol. 39, no. 11, pp. 1118–1127, 2012. View at Publisher · View at Google Scholar
  • Evgeny Kanshin, Stephen Michnick, and Pierre Thibault, “Sample preparation and analytical strategies for large-scale phosphoproteomics experiments,” Seminars In Cell & Developmental Biology, vol. 23, no. 8, pp. 843–853, 2012. View at Publisher · View at Google Scholar
  • Claudio Nicolini, Nicola Bragazzi, and Eugenia Pechkova, “Nanoproteomics enabling personalized nanomedicine,” Advanced Drug Delivery Reviews, vol. 64, no. 13, pp. 1522–1531, 2012. View at Publisher · View at Google Scholar
  • Cristina Barsan, Mondher Bouzayen, Alain Latché, Jean-Claude Pech, Mohamed Zouine, Elie Maza, Wanping Bian, Isabel Egea, Michel Rossignol, David Bouyssie, Carole Pichereaux, and Eduardo Purgatto, “Proteomic analysis of chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled with disrupted thylakoid biogenesis machinery and elevated energy-production components.,” Plant physiology, vol. 160, no. 2, pp. 708–25, 2012. View at Publisher · View at Google Scholar
  • Chongyang Li, Qian Xiong, Jia Zhang, Feng Ge, and Li-Jun Bi, “Quantitative proteomic strategies for the identification of microRNA targets,” Expert Review Of Proteomics, vol. 9, no. 5, pp. 549–559, 2012. View at Publisher · View at Google Scholar
  • Ming-Quan Guo, and Bill X. Huang, “Liquid Chromatography and Mass Spectrometry (LC-MS) Based Strategies for Quantitative Phosphoproteomics,” Current Analytical Chemistry, vol. 8, no. 1, pp. 3–21, 2012. View at Publisher · View at Google Scholar
  • Hongxia Wang, Sophie Alvarez, and Leslie M. Hicks, “Comprehensive Comparison of iTRAQ and Label-free LC-Based Quantitative Proteomics Approaches Using Two Chlamydomonas reinhardtii Strains of Interest for Biofuels Engineering,” Journal Of Proteome Research, vol. 11, no. 1, pp. 487–501, 2012. View at Publisher · View at Google Scholar
  • Raquel Gonzalez-Fernandez, and Jesus V. Jorrin-Novo, “Contribution of Proteomics to the Study of Plant Pathogenic Fungi,” Journal of Proteome Research, vol. 11, no. 1, pp. 3–16, 2012. View at Publisher · View at Google Scholar
  • Andrew N. Stephens, Luk J. F. Rombauts, and Lois A. Salamonsen, “Diagnosis of Endometriosis: Proteomics,” Endometriosis, pp. 324–335, 2012. View at Publisher · View at Google Scholar
  • Amy Hye Won Jeon, and Gerold Schmitt-Ulms, “Time-Controlled transcardiac perfusion crosslinking for in vivo interactome studies,” Methods in Molecular Biology, vol. 803, pp. 231–246, 2012. View at Publisher · View at Google Scholar
  • Margarita Villar, Marina Popara, Elena Bonzon-Kulichenko, Nieves Ayllon, Jesus Vazquez, and Jose de la Fuente, “Characterization of the tick-pathogen interface by quantitative proteomics,” Ticks and Tick-Borne Diseases, vol. 3, no. 3, pp. 154–158, 2012. View at Publisher · View at Google Scholar
  • Stephanie D. Byrum, Charity L. Washam, Corey O. Montgomery, Alan J. Tackett, and Larry J. Suva, “Proteomic Technologies for the Study of Osteosarcoma,” Sarcoma, vol. 2012, pp. 1–10, 2012. View at Publisher · View at Google Scholar
  • Thomas Rydzak, Richard Sparling, Peter D. McQueen, Oleg V. Krokhin, Vic Spicer, Peyman Ezzati, Ravi C. Dwivedi, Dmitry Shamshurin, David B. Levin, and John A. Wilkins, “Proteomic analysis of Clostridium thermocellum core metabolism: Relative protein expression profiles and growth phase-dependent changes in protein expression,” BMC Microbiology, vol. 12, 2012. View at Publisher · View at Google Scholar
  • Kevin L. Schauer, Dana M. Freund, Jessica E. Prenni, and Norman P. Curthoys, “Proteomic profiling and pathway analysis of the response of rat renal proximal convoluted tubules to metabolic acidosis,” American Journal of Physiology - Renal Physiology, vol. 305, no. 5, pp. F628–F640, 2013. View at Publisher · View at Google Scholar
  • Carrie E. Rubel, Jonathan C. Schisler, Eric D. Hamlett, Robert M. DeKroon, Mathias Gautel, Oscar Alzate, and Cam Patterson, “Diggin′ on U(biquitin): A Novel Method for the Identification of Physiological E3 Ubiquitin Ligase Substrates,” Cell Biochemistry and Biophysics, vol. 67, no. 1, pp. 127–138, 2013. View at Publisher · View at Google Scholar
  • Eduardo J. Pilau, Amadeu H. Iglesias, and Fabio C. Gozzo, “A new label-free approach for the determination of reaction rates in oxidative footprinting experiments,” Analytical and Bioanalytical Chemistry, vol. 405, no. 24, pp. 7679–7686, 2013. View at Publisher · View at Google Scholar
  • Steven L. Wood, Jules A. Westbrook, and Janet E. Brown, “Omic-profiling in breast cancer metastasis to bone: Implications for mechanisms, biomarkers and treatment,” Cancer Treatment Reviews, 2013. View at Publisher · View at Google Scholar
  • Adam R. Evans, “Proteomics quantification of protein nitration,” Reviews in Analytical Chemistry, vol. 32, no. 3, pp. 173–187, 2013. View at Publisher · View at Google Scholar
  • Carly I. Dix, Harish Chandra Soundararajan, Nikola S. Dzhindzhev, Farida Begum, Beat Suter, Hiroyuki Ohkura, Elaine Stephens, and Simon L. Bullock, “Lissencephaly-1 promotes the recruitment of dynein and dynactin to transported mRNAs,” Journal of Cell Biology, vol. 202, no. 3, pp. 479–494, 2013. View at Publisher · View at Google Scholar
  • Helena Kupcova Skalnikova, “Proteomic Techniques for Characterisation of Mesenchymal Stem Cell Secretome,” Biochimie, 2013. View at Publisher · View at Google Scholar
  • Brian C. Gau, Jiawei Chen, and Michael L. Gross, “Fast photochemical oxidation of proteins for comparing solvent-accessibility changes accompanying protein folding: Data processing and application to barstar,” Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol. 1834, no. 6, pp. 1230–1238, 2013. View at Publisher · View at Google Scholar
  • Chunchao Zhang, Yifan Liu, and Philip C. Andrews, “Quantification of histone modifications using 15N metabolic labeling,” Methods, vol. 61, no. 3, pp. 236–243, 2013. View at Publisher · View at Google Scholar
  • Dongyan Hou, Ying Chen, Jiamei Liu, Lin Xu, Zhiyong Zhang, Juan Zhang, Hua Wang, Xin Wang, Jin Chen, Rongrui Zhao, Aihua Hu, Hakon Hakonarson, Lin Zhang, and Yan Shen, “Proteomics screen to reveal molecular changes mediated by C722G missense mutation in CHRM2 gene,” Journal of Proteomics, 2013. View at Publisher · View at Google Scholar
  • Leticia Mora, Peter M. Bramley, and Paul D. Fraser, “Development and optimisation of a label-free quantitative proteomic procedure and its application in the assessment of genetically modified tomato fruit,” Proteomics, vol. 13, no. 12-13, pp. 2016–2030, 2013. View at Publisher · View at Google Scholar
  • Marianne Sandin, Ashfaq Ali, Karin Hansson, Olle Månsson, Erik Andreasson, Svante Resjö, and Fredrik Levander, “An adaptive alignment algorithm for quality-controlled label-free LC-MS,” Molecular and Cellular Proteomics, vol. 12, no. 5, pp. 1407–1420, 2013. View at Publisher · View at Google Scholar
  • Paul D. Piehowski, David G. Camp, Richard D. Smith, Amanda J. Myers, Vladislav A. Petyuk, Daniel J. Orton, Fang Xie, Ronald J. Moore, Manuel Ramirez-Restrepo, Anzhelika Engel, Andrew P. Lieberman, and Roger L. Albin, “Sources of technical variability in quantitative LC-MS proteomics: Human brain tissue sample analysis,” Journal of Proteome Research, vol. 12, no. 5, pp. 2128–2137, 2013. View at Publisher · View at Google Scholar
  • Dana M. Freund, and Jessica E. Prenni, “Improved detection of quantitative differences using a combination of spectral counting and MS/MS total ion current,” Journal of Proteome Research, vol. 12, no. 4, pp. 1996–2004, 2013. View at Publisher · View at Google Scholar
  • Fatemeh Babaei, Rajkumar Ramalingam, Amy Tavendale, Yimin Liang, Leo So Kin Yan, Paul Ajuh, Shuk Han Cheng, and Yun Wah Lam, “Novel blood collection method allows plasma proteome analysis from single zebrafish,” Journal of Proteome Research, vol. 12, no. 4, pp. 1580–1590, 2013. View at Publisher · View at Google Scholar
  • Susan Fanayan, Joshua T. Smith, Ling Y. Lee, Fangfei Yan, Michael Snyder, William S. Hancock, and Edouard Nice, “Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405,” Journal of Proteome Research, vol. 12, no. 4, pp. 1732–1742, 2013. View at Publisher · View at Google Scholar
  • Raqual Bower, Douglas Tritschler, Kristyn VanderWaal, Catherine A. Perrone, Joshua Mueller, Laura Fox, Winfield S. Sale, and M.E. Porter, “The N-DRC forms a conserved biochemical complex that maintains outer doublet alignment and limits microtubule sliding in motile axonemes,” Molecular Biology of the Cell, vol. 24, no. 8, pp. 1134–1152, 2013. View at Publisher · View at Google Scholar
  • Caroline Marcon, Tobias Lamkemeyer, Waqas Ahmed Malik, Denise Ungrue, Hans-Peter Piepho, and Frank Hochholdinger, “Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC–MS,” Journal of Proteomics, 2013. View at Publisher · View at Google Scholar
  • Leroi V. DeSouza, and K.W. Michael Siu, “Mass spectrometry-based quantification,” Clinical Biochemistry, vol. 46, no. 6, pp. 421–431, 2013. View at Publisher · View at Google Scholar
  • Rachel A. Craven, and Naveen S. Vasudev, “Proteomics and the search for biomarkers for renal cancer,” Clinical Biochemistry, vol. 46, no. 6, pp. 456–465, 2013. View at Publisher · View at Google Scholar
  • Catherine E. Vincent, Gregory K. Potts, Arne Ulbrich, Michael S. Westphall, James A. Atwood, Joshua J. Coon, and D. Brent Weatherly, “Segmentation of Precursor Mass Range Using "Tiling" Approach Increases Peptide Identifications for MS1-Based Label-Free Quantification,” Analytical Chemistry, vol. 85, no. 5, pp. 2825–2832, 2013. View at Publisher · View at Google Scholar
  • María del Carmen Mena, and Juan Pablo Albar, “Next Generation Instruments and Methods for Proteomics,” Foodomics, pp. 15–67, 2013. View at Publisher · View at Google Scholar
  • Derek R. Stein, Adam Burgener, and Terry Blake Ball, “Proteomics as a novel HIV immune monitoring tool,” Current Opinion in HIV and AIDS, vol. 8, no. 2, pp. 140–146, 2013. View at Publisher · View at Google Scholar
  • Brenna McJury Richardson, Erik J. Soderblom, J. Will Thompson, and M. Arthur Moseley, “Automated, reproducible, titania-based phosphopeptide enrichment strategy for label-free quantitative phosphoproteomics,” Journal of Biomolecular Techniques, vol. 24, no. 1, pp. 8–16, 2013. View at Publisher · View at Google Scholar
  • Daniela Cretu, Eleftherios P. Diamandis, and Vinod Chandran, “Delineating the synovial fluid proteome: Recent advancements and ongoing challenges in biomarker research,” Critical Reviews in Clinical Laboratory Sciences, vol. 50, no. 2, pp. 51–63, 2013. View at Publisher · View at Google Scholar
  • Steven L. Ponicsan, Stephane Houel, William M. Old, Natalie G. Ahn, James A. Goodrich, and Jennifer F. Kugel, “The Non-Coding B2 RNA Binds to the DNA Cleft and Active-Site Region of RNA Polymerase II,” Journal of Molecular Biology, 2013. View at Publisher · View at Google Scholar
  • Izabela Sokolowska, Armand G. Ngounou Wetie, Kelly Wormwood, Johannes Thome, Costel C. Darie, and Alisa G. Woods, “The potential of biomarkers in psychiatry: focus on proteomics,” Journal of Neural Transmission, 2013. View at Publisher · View at Google Scholar
  • Monika Koehnke, Christine Delon, Marcus L. Hastie, Uyen T. T. Nguyen, Yao-Wen Wu, Herbert Waldmann, Roger S. Goody, Jeffrey J. Gorman, and Kirill Alexandrov, “Rab GTPase Prenylation Hierarchy and Its Potential Role in Choroideremia Disease,” Plos One, vol. 8, no. 12, 2013. View at Publisher · View at Google Scholar
  • Xianyu Li, Jing Jiang, Xinyuan Zhao, Jifeng Wang, Huanhuan Han, Yan Zhao, Bo Peng, Rugang Zhong, Wantao Ying, and Xiaohong Qian, “N-glycoproteome Analysis of the Secretome of Human Metastatic Hepatocellular Carcinoma Cell Lines Combining Hydrazide Chemistry, HILIC Enrichment and Mass Spectrometry,” Plos One, vol. 8, no. 12, 2013. View at Publisher · View at Google Scholar
  • Jakob Vowinckel, Floriana Capuano, Kate Campbell, Michael J. Deery, Kathryn S. Lilley, and Markus Ralser, “The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics,” F1000Research, vol. 2, pp. 272, 2013. View at Publisher · View at Google Scholar
  • Matthew R. Russell, Brahim Achour, Edward A. Mckenzie, Ruth Lopez, Matthew D. Harwood, Amin Rostami-Hodjegan, and Jill Barber, “Alternative Fusion Protein Strategies to Express Recalcitrant QconCAT Proteins for Quantitative Proteomics of Human Drug Metabolizing Enzymes and Transporters,” Journal of Proteome Research, vol. 12, no. 12, pp. 5934–5942, 2013. View at Publisher · View at Google Scholar
  • Leslie C. Timpe, Roger Yen, Nicole V. Haste, Christina Litsakos-Cheung, Ten-Yang Yen, and Bruce A. Macher, “Systemic alteration of cell-surface and secreted glycoprotein expression in malignant breast cancer cell lines,” Glycobiology, vol. 23, no. 11, pp. 1240–1249, 2013. View at Publisher · View at Google Scholar
  • Jing Qin, Mulin Jun Li, Panwen Wang, Nai Sum Wong, Maria P. Wong, Zhengyuan Xia, George S. W. Tsao, Michael Q. Zhang, and Junwen Wang, “ProteoMirExpress: Inferring MicroRNA and Protein-centered Regulatory Networks from High-throughput Proteomic and mRNA Expression Data,” Molecular & Cellular Proteomics, vol. 12, no. 11, pp. 3379–3387, 2013. View at Publisher · View at Google Scholar
  • Guido Mastrobuoni, Huili Qiao, Immacolata Iovinella, Simona Sagona, Alberto Niccolini, Francesca Boscaro, Beniamino Caputo, Marta R. Orejuela, Alessandra della Torre, Stefan Kempa, Antonio Felicioli, Paolo Pelosi, Gloriano Moneti, and Francesca Romana Dani, “A Proteomic Investigation of Soluble Olfactory Proteins in Anopheles gambiae,” Plos One, vol. 8, no. 11, 2013. View at Publisher · View at Google Scholar
  • David W. Greening, Hong Ji, Eugene A. Kapp, and Richard J. Simpson, “Sulindac modulates secreted protein expression from LIM1215 colon carcinoma cells prior to apoptosis,” Biochimica et Biophysica Acta-Proteins and Proteomics, vol. 1834, no. 11, pp. 2293–2307, 2013. View at Publisher · View at Google Scholar
  • Joe Swift, Takamasa Harada, Amnon Buxboim, Jae-Won Shin, Hsin-Yao Tang, David W Speicher, and Dennis E Discher, “Label-free mass spectrometry exploits dozens of detected peptides to quantify lamins in wildtype and knockdown cells,” Nucleus, vol. 4, no. 6, pp. 450–459, 2013. View at Publisher · View at Google Scholar
  • Barbara Deracinois, Christophe Flahaut, Sophie Duban-Deweer, and Yannis Karamanos, “Comparative and Quantitative Global Proteomics Approaches: An Overview,” Proteomes, vol. 1, no. 3, pp. 180–218, 2013. View at Publisher · View at Google Scholar
  • Archana Bharadwaj Siva, Priyanka Srivastava, and Sisinthy Shivaji, “Understanding the pathogenesis of endometriosis through proteomics: Recent advances and future prospects,” PROTEOMICS - Clinical Applications, 2013. View at Publisher · View at Google Scholar
  • O. Alejandro Balbin, John R. Prensner, Anirban Sahu, Anastasia Yocum, Sunita Shankar, Rohit Malik, Damian Fermin, Saravana M. Dhanasekaran, Benjamin Chandler, Dafydd Thomas, David G. Beer, Xuhong Cao, Alexey I. Nesvizhskii, and Arul M. Chinnaiyan, “Reconstructing targetable pathways in lung cancer by integrating diverse omics data,” Nature Communications, vol. 4, 2013. View at Publisher · View at Google Scholar
  • Laetitia Theron, Xavier Fernandez, Nathalie Marty-Gasset, Christophe Chambon, Didier Viala, Carole Pichereaux, Michel Rossignol, Thierry Astruc, and Caroline Molette, “Proteomic Analysis of Duck Fatty Liver during Post-Mortem Storage Related to the Variability of Fat Loss during Cooking of “Foie Gras”,” Journal of Agricultural and Food Chemistry, vol. 61, no. 4, pp. 920–930, 2013. View at Publisher · View at Google Scholar
  • Sun, and He, “Chemical proteomics to identify molecular targets of small compounds,” Current Molecular Medicine, vol. 13, no. 7, pp. 1175–1191, 2013. View at Publisher · View at Google Scholar
  • Hans K. Carlson, Iain C. Clark, Steven J. Blazewicz, Anthony T. Iavarone, and John D. Coates, “Fe(II) oxidation is an innate capability of nitrate-reducing bacteria that involves abiotic and biotic reactions,” Journal of Bacteriology, vol. 195, no. 14, pp. 3260–3268, 2013. View at Publisher · View at Google Scholar
  • Ju Bai, Aili He, Wanggang Zhang, Chen Huang, Juan Yang, Yun Yang, Jianli Wang, and Yang Zhang, “Potential biomarkers for adult acute myeloid leukemia minimal residual disease assessment searched by serum peptidome profiling,” Proteome Science, vol. 11, no. 1, pp. 39, 2013. View at Publisher · View at Google Scholar
  • Valerie C. Wasinger, Ming Zeng, and Yunki Yau, “Current Status and Advances in Quantitative Proteomic Mass Spectrometry,” International Journal of Proteomics, vol. 2013, pp. 1–12, 2013. View at Publisher · View at Google Scholar
  • Hercules Moura, Rebecca R. Terilli, Adrian R. Woolfitt, Yulanda M. Williamson, Glauber Wagner, Thomas A. Blake, Maria I. Solano, and John R. Barr, “Proteomic Analysis and Label-Free Quantification of the Large Clostridium difficile Toxins,” International Journal of Proteomics, vol. 2013, pp. 1–10, 2013. View at Publisher · View at Google Scholar
  • Hung V Trinh, Jonas Grossmann, Peter Gehrig, Bernd Roschitzki, Ralph Schlapbach, Urs F Greber, and Silvio Hemmi, “iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections.,” International journal of proteomics, vol. 2013, pp. 581862, 2013. View at Publisher · View at Google Scholar
  • Xianyin Lai, Lianshui Wang, and Frank A. Witzmann, “Issues and Applications in Label-Free Quantitative Mass Spectrometry,” International Journal of Proteomics, vol. 2013, pp. 1–13, 2013. View at Publisher · View at Google Scholar
  • Debasish Paul, Avinash Kumar, Akshada Gajbhiye, Manas K. Santra, and Rapole Srikanth, “Mass Spectrometry-Based Proteomics in Molecular Diagnostics: Discovery of Cancer Biomarkers Using Tissue Culture,” BioMed Research International, vol. 2013, pp. 1–16, 2013. View at Publisher · View at Google Scholar
  • Can Bruce, Kathryn Stone, Erol Gulcicek, and Kenneth Williams, “Proteomics and the analysis of proteomic data: 2013 overview of current protein-profiling technologies,” Current Protocols in Bioinformatics, no. 41, 2013. View at Publisher · View at Google Scholar
  • Jean L. Spencer, Vivek N. Bhatia, Stephen A. Whelan, Catherine E. Costello, and Mark E. McComb, “STRAP PTM: Software tool for rapid annotation and differential comparison of protein post-translational modifications,” Current Protocols in Bioinformatics, no. 44, 2013. View at Publisher · View at Google Scholar
  • Susan K. Van Riper, Ebbing P. De Jong, John V. Carlis, and Timothy J. Griffin, “Mass spectrometry-based proteomics: Basic principles and emerging technologies and directions,” Advances in Experimental Medicine and Biology, vol. 990, pp. 1–35, 2013. View at Publisher · View at Google Scholar
  • Christina Loosse, Katrin Marcus, and Bodo Schoenebeck, “Principles of proteomic approaches to the cytoskeleton,” Neuromethods, vol. 79, pp. 85–116, 2013. View at Publisher · View at Google Scholar
  • Susan K. Van Riper, Ebbing P. de Jong, John V. Carlis, and Timothy J. Griffin, “Mass Spectrometry-Based Proteomics: Basic Principles and Emerging Technologies and Directions,” Radiation Proteomics: The Effects of Ionizing and Non-Ionizing Radiation On, vol. 990, pp. 1–35, 2013. View at Publisher · View at Google Scholar
  • Susan K. Van Riper, Ebbing P. De Jong, John V. Carlis, and Timothy J. Griffin, “Mass spectrometry-based proteomics: Basic principles and emerging technologies and directions,” Advances in Experimental Medicine and Biology, vol. 990, pp. 1–35, 2013. View at Publisher · View at Google Scholar
  • Qiang Shao, Alan J. Tackett, Ling Gao, Stephanie D. Byrum, Linley E. Moreland, Samuel G. Mackintosh, Aarthi Kannan, Zhenyu Lin, Michael Morgan, Brendan C. Stack Jr., and Lynn A. Cornelius, “A proteomic study of human merkel cell carcinoma,” Journal of Proteomics and Bioinformatics, vol. 6, no. 11, pp. 275–282, 2013. View at Publisher · View at Google Scholar
  • Tushar Dilipchand Lodha, Padmalochan Hembram, and Nitile Tep, Jolly Basak, “Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction,” American Journal of Plant Sciences, vol. 04, no. 06, pp. 1212–1226, 2013. View at Publisher · View at Google Scholar
  • Craig Russell, Ayesha Rahman, and Afzal R. Mohammed, “Application of genomics, proteomics and metabolomics in drug discovery, development and clinic,” Therapeutic Delivery, vol. 4, no. 3, pp. 395–413, 2013. View at Publisher · View at Google Scholar
  • Xuefei Yin, Xiaohui Liu, Yang Zhang, Guoquan Yan, Fang Wang, Haojie Lu, Huali Shen, and Pengyuan Yang, “Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation,” Proteomics, vol. 14, no. 17-18, pp. 2008–2016, 2014. View at Publisher · View at Google Scholar
  • Yuetian Yan, Guodong Chen, Hui Wei, Richard Y.-C. Huang, Jingjie Mo, Don L. Rempel, Adrienne A. Tymiak, and Michael L. Gross, “Fast Photochemical Oxidation of Proteins (FPOP) Maps the Epitope of EGFR Binding to Adnectin,” Journal of The American Society for Mass Spectrometry, 2014. View at Publisher · View at Google Scholar
  • Esther Nkuipou-Kenfack, Thomas Koeck, Harald Mischak, Andreas Pich, Joost P. Schanstra, Petra Zürbig, and Björn Schumacher, “Proteome analysis in the assessment of ageing,” Ageing Research Reviews, 2014. View at Publisher · View at Google Scholar
  • Qihui Wang, Yixiang Duan, Qingyu Lin, and Qiaoling Yu, “Emerging salivary biomarkers by mass spectrometry,” Clinica Chimica Acta, vol. 438, pp. 214–221, 2014. View at Publisher · View at Google Scholar
  • Jonathan Ashby, Kenneth Flack, Luis A. Jimenez, Yaokai Duan, Abdel-Kareem Khatib, George Somlo, Shizhen Emily Wang, Xinping Cui, and Wenwan Zhong, “Distribution Profiling of Circulating MicroRNAs in Serum,” Analytical Chemistry, vol. 86, no. 18, pp. 9343–9349, 2014. View at Publisher · View at Google Scholar
  • Vishvanath Tiwari, and Monalisa Tiwari, “Quantitative proteomics to study carbapenenn resistance in Acinetobacter baumannii,” Frontiers in Microbiology, vol. 5, 2014. View at Publisher · View at Google Scholar
  • Nabila Aboulaich, Wai Keen Chung, Jenny Heidbrink Thompson, Christopher Larkin, David Robbins, and Min Zhu, “A novel approach to monitor clearance of host cell proteins associated with monoclonal antibodies,” Biotechnology Progress, 2014. View at Publisher · View at Google Scholar
  • Xiaomeng Shen, Rebeccah Young, John M. Canty, and Jun Qu, “Quantitative proteomics in cardiovascular research: Global and targeted strategies,” PROTEOMICS - Clinical Applications, 2014. View at Publisher · View at Google Scholar
  • Nardin Samuel, Marc Remke, James T. Rutka, Brian Raught, and David Malkin, “Proteomic analyses of CSF aimed at biomarker development for pediatric brain tumors,” Journal of Neuro-Oncology, vol. 118, no. 2, pp. 225–238, 2014. View at Publisher · View at Google Scholar
  • John C. Dreixler, Jacqueline N. Poston, Irina Balyasnikova, Afzhal R. Shaikh, Kelsey Y. Tupper, Sineadh Conway, Venkat Boddapati, Marcus M. Marcet, Maciej S. Lesniak, and Steven Roth, “Delayed Administration of Bone Marrow Mesenchymal Stem Cell Conditioned Medium Significantly Improves Outcome After Retinal Ischemia in Rats,” Investigative Ophthalmology & Visual Science, vol. 55, no. 6, pp. 3785–3796, 2014. View at Publisher · View at Google Scholar
  • Stefanie Huegel, Reinhard Depping, Gunnar Dittmar, Franziska Rother, Ryan Cabot, Matthias D. Sury, Enno Hartmann, and Michael Bader, “Identification of Importin alpha 7 Specific Transport Cargoes Using a Proteomic Screening Approach,” Molecular & Cellular Proteomics, vol. 13, no. 5, pp. 1286–1298, 2014. View at Publisher · View at Google Scholar
  • George S. Karagiannis, Maria P. Pavlou, Punit Saraon, Natasha Musrap, Annie Xie, Ihor Batruch, Ioannis Prassas, Apostolos Dimitromanolakis, Constantina Petraki, and Eleftherios P. Diamandis, “In-depth proteomic delineation of the colorectal cancer exoproteome: Mechanistic insight and identification of potential biomarkers,” Journal of Proteomics, vol. 103, pp. 121–136, 2014. View at Publisher · View at Google Scholar
  • Wen-Jun Tu, Xiao-Ye Liu, Hao Dong, Yan Yu, Yi Wang, and Hui Chen, “Phosphatidylinositol-3,4,5-Trisphosphate 5-Phosphatase 1: A Meaningful and Independent Marker to Predict Stroke in the Chinese Population,” Journal of Molecular Neuroscience, vol. 52, no. 4, pp. 507–514, 2014. View at Publisher · View at Google Scholar
  • Mélanie Abonnenc, and Manuel Mayrpp. 249–266, 2014. View at Publisher · View at Google Scholar
  • David M. Blodgett, Anthony J. Cura, and David M. Harlan, “The pancreatic β-cell transcriptome and integrated-omics,” Current Opinion in Endocrinology & Diabetes and Obesity, vol. 21, no. 2, pp. 83–88, 2014. View at Publisher · View at Google Scholar
  • Markus Ralser, Jakob Vowinckel, Floriana Capuano, Kate Campbell, Michael J. Deery, and Kathryn S. Lilley, “The beauty of being (label)-free: Sample preparation methods for SWATH-MS and next-generation targeted proteomics,” F1000Research, vol. 2, 2014. View at Publisher · View at Google Scholar
  • M. Pooladi, S. K. R. Abad, and M. Hashemi, “Proteomics analysis of human brain glial cell proteome by 2D gel,” Indian Journal of Cancer, vol. 51, no. 2, pp. 159–162, 2014. View at Publisher · View at Google Scholar
  • Benedetta Turriziani, Amaya Garcia-Munoz, Ruth Pilkington, Cinzia Raso, Walter Kolch, and Alexander von Kriegsheim, “On-Beads Digestion in Conjunction with Data-Dependent Mass Spectrometry: A Shortcut to Quantitative and Dynamic Interaction Proteomics,” Biology, vol. 3, no. 2, pp. 320–332, 2014. View at Publisher · View at Google Scholar
  • Maurijn Y. Kessels, Leonie F. A. Huitema, Sjef Boeren, Sander Kranenbarg, Stefan Schulte-Merker, and Johan L. van Leeuwen, “Proteomics Analysis of the Zebrafish Skeletal Extracellular Matrix,” Plos One, vol. 9, no. 3, 2014. View at Publisher · View at Google Scholar
  • Sahyun Hong, Injun Cha, Nan-Ok Kim, Jong-Bok Seo, Soo-Young Kim, Jong-Hyun Kim, Gyung Tae Chung, Byeonghwa Jeon, and Yeon-Ho Kang, “Comparative Proteomic Label-Free Analysis of Campylobacter jejuni NCTC 11168 Cultured with Porcine Mucin,” Foodborne Pathogens and Disease, vol. 11, no. 3, pp. 240–247, 2014. View at Publisher · View at Google Scholar
  • Rui Luo, Liurong Fang, Hui Jin, Dang Wang, Kang An, Ningzhi Xu, Huanchun Chen, and Shaobo Xiao, “Label-Free Quantitative Phosphoproteomic Analysis Reveals Differentially Regulated Proteins and Pathway in PRRSV-Infected Pulmonary Alveolar Macrophages,” Journal of Proteome Research, vol. 13, no. 3, pp. 1270–1280, 2014. View at Publisher · View at Google Scholar
  • Omid Azimzadeh, and Michael J. Atkinson, “Proteomics in radiation research: present status and future perspectives,” Radiation and Environmental Biophysics, vol. 53, no. 1, pp. 31–38, 2014. View at Publisher · View at Google Scholar
  • F. Cynthia Martin, Monika Hiller, Pietro Spitali, Stijn Oonk, Hans Dalebout, Magnus Palmblad, Amina Chaouch, Michela Guglieri, Volker Straub, Hanns Lochmüller, Erik H. Niks, Jan J. G. M. Verschuuren, Annemieke Aartsma-Rus, André M. Deelder, Yuri E. M. van der Burgt, and Peter A. C. 't Hoen, “Fibronectin is a serum biomarker for Duchenne muscular dystrophy,” PROTEOMICS - Clinical Applications, 2014. View at Publisher · View at Google Scholar
  • Tainah Silva Galdino, Rubem Figueiredo Sadok Menna-Barreto, Constança Britto, Franklyn Samudio, Adeilton Brandão, and Dário Eluan Kalume, “Cell disruption using a different methodology for proteomics analysis of Trypanosoma cruzi strains,” Analytical Biochemistry, vol. 448, pp. 1–8, 2014. View at Publisher · View at Google Scholar
  • Shuguang Zhang, Xiaolong Cao, Yan He, Steve Hartson, and Haobo Jiang, “Semi-quantitative analysis of changes in the plasma peptidome of Manduca sexta larvae and their correlation with the transcriptome variations upon immune challenge,” Insect Biochemistry and Molecular Biology, 2014. View at Publisher · View at Google Scholar
  • A Atrih, M A V Mudaliar, P Zakikhani, D J Lamont, J T-J Huang, S E Bray, G Barton, S Fleming, and G Nabi, “Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling,” British Journal of Cancer, 2014. View at Publisher · View at Google Scholar
  • Syafrizayanti Syafrizayanti, Christian Betzen, Joerg D. Hoheisel, and Damjana Kastelic, “Methods for analyzing and quantifying protein-protein interaction,” Expert Review of Proteomics, vol. 11, no. 1, pp. 107–120, 2014. View at Publisher · View at Google Scholar
  • Hui Li, Chunmei Liu, Mugizi Robert Rwebangira, and Legand Burge, “Mono-isotope prediction for mass spectra using Bayes network,” Tsinghua Science and Technology, vol. 19, no. 6, pp. 617–623, 2014. View at Publisher · View at Google Scholar
  • Junying Wei, Fangbo Zhang, Yi Zhang, Chunyu Cao, Xianyu Li, Defeng Li, Xin Liu, Hongjun Yang, and Luqi Huang, “Proteomic Investigation of Signatures for Geniposide-Induced Hepatotoxicity,” Journal Of Proteome Research, vol. 13, no. 12, pp. 5724–5733, 2014. View at Publisher · View at Google Scholar
  • Virginie Licker, and Pierre R. Burkhard, “Proteomics as a new paradigm to tackle Parkinson’s disease research challenges,” Translational Proteomics, vol. 4-5, pp. 1–17, 2014. View at Publisher · View at Google Scholar
  • Sergei Nekhai, and Marina Jerebtsova, “Quantitative mass spectrometry of urinary biomarkers,” Journal of Integrated OMICS, vol. 4, no. 2, pp. 69–78, 2014. View at Publisher · View at Google Scholar
  • Hsin-Pin Ho, Pratikkumar Rathod, Marissa Louis, Christine K. Tada, Sherida Rahaman, Kevin J. Mark, Jin Leng, Dibyendu Dana, Sanjai Kumar, Mathias Lichterfeld, and Emmanuel J. Chang, “Studies on quantitative phosphopeptide analysis by matrix-assisted laser desorption/ionization mass spectrometry without label, chromatography or calibration curves,” Rapid Communications in Mass Spectrometry, vol. 28, no. 24, pp. 2681–2689, 2014. View at Publisher · View at Google Scholar
  • Brian D. Cholewa, Molly C. Pellitteri-Hahn, Cameron O. Scarlett, and Nihal Ahmad, “Large-Scale Label-Free Comparative Proteomics Analysis of Polo-Like Kinase 1 Inhibition via the Small-Molecule Inhibitor BI 6727 (Volasertib) in BRAF(V600E) Mutant Melanoma Cells,” Journal of Proteome Research, vol. 13, no. 11, pp. 5041–5050, 2014. View at Publisher · View at Google Scholar
  • Ken Aoshima, Kentaro Takahashi, Masayuki Ikawa, Takayuki Kimura, Mitsuru Fukuda, Satoshi Tanaka, Howell E. Parry, Yuichiro Fujita, Akiyasu C. Yoshizawa, Shin-ichi Utsunomiya, Shigeki Kajihara, Koichi Tanaka, and Yoshiya Oda, “A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry,” Bmc Bioinformatics, vol. 15, 2014. View at Publisher · View at Google Scholar
  • Dieter M Drexler, Timothy V. Olah, Michael D. Reily, Petia A. Shipkova, Holly D. Soares, and Adrienne A. Tymiakpp. 182–199, 2014. View at Publisher · View at Google Scholar
  • Hailong Wang, Yan Li, Lijuan Yang, Baofeng Yu, Ping Yan, Min Pang, Xiaobing Li, Hong Yang, Guoping Zheng, Jun Xie, and Rui Guo, “Mass spectrometry-based, label-free quantitative proteomics of round spermatids in mice,” Molecular Medicine Reports, vol. 10, no. 4, pp. 2009–2024, 2014. View at Publisher · View at Google Scholar
  • Giorgio Gorini, R. Adron Harris, and R. Dayne Mayfield, “Proteomic Approaches and Identification of Novel Therapeutic Targets for Alcoholism,” Neuropsychopharmacology, vol. 39, no. 1, pp. 104–130, 2014. View at Publisher · View at Google Scholar
  • Erhan Kenar, Holger Franken, Sara Forcisi, Kilian Woermann, Hans-Ulrich Haering, Rainer Lehmann, Philippe Schmitt-Kopplin, and Andreas Zell, “Metabolites from Liquid Chromatography-Mass Spectrometry Data,” Molecular & Cellular Proteomics, vol. 13, no. 1, pp. 348–359, 2014. View at Publisher · View at Google Scholar
  • Laetitia Theron, Marine Gueugneau, Cecile Coudy, Didier Viala, Astrid Bijlsma, Gillian Butler-Browne, Andrea Maier, Daniel Bechet, and Christophe Chambon, “Label-free Quantitative Protein Profiling of vastus lateralis Muscle During Human Aging,” Molecular & Cellular Proteomics, vol. 13, no. 1, pp. 283–294, 2014. View at Publisher · View at Google Scholar
  • Christian Schoeneich, Elena Dremina, Nadezhda Galeva, and Victor Sharov, “Apoptosis in differentiating C2C12 muscle cells selectively targets Bcl-2-deficient myotubes,” Apoptosis, vol. 19, no. 1, pp. 42–57, 2014. View at Publisher · View at Google Scholar
  • Bruce R. Southey, Ji Eun Lee, Leonid Zamdborg, Norman Atkins, Jennifer W. Mitchell, Mingxi Li, Martha U. Gillette, Neil L. Kelleher, and Jonathan V. Sweedler, “Comparing Label-Free Quantitative Peptidomics Approaches to Characterize Diurnal Variation of Peptides in the Rat Suprachiasmatic Nucleus,” Analytical Chemistry, vol. 86, no. 1, pp. 443–452, 2014. View at Publisher · View at Google Scholar
  • Adam J. McShane, Vahid Farrokhi, Reza Nemati, Song Li, and Xudong Yao, “An Overview of Quantitative Proteomic Approaches,” Fundamentals of Advanced Omics Technologies: From Genes to Metabolites, vol. 63, pp. 111–135, 2014. View at Publisher · View at Google Scholar
  • Sayani Dasgupta, and Lloyd D. Fricker, “High-Resolution Analytical Tools for Quantitative Peptidomics,” Comprehensive Analytical Chemistry, vol. 63, pp. 305–324, 2014. View at Publisher · View at Google Scholar
  • Holger Husi, and Amaya Albalat, “Proteomics,” Handbook of Pharmacogenomics and Stratified Medicine, pp. 147–179, 2014. View at Publisher · View at Google Scholar
  • Chao Pan, Wenxian Peng, Huilong Duan, and Ning Deng, “Complex Proteomes Analysis Using Label-Free Mass Spectrometry-Based Quantitative Approach Coupled with Biomedical Knowledge,” Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications, vol. 8827, pp. 20–28, 2014. View at Publisher · View at Google Scholar
  • Tiago S. Balbuena, Diogo Ribeiro Demartini, and Jay J. Thelen, “Global quantitative proteomics using spectral counting: An inexpensive experimental and bioinformatics workflow for deep proteome coverage,” Methods in Molecular Biology, vol. 1072, pp. 171–183, 2014. View at Publisher · View at Google Scholar
  • Tiago S. Balbuena, Diogo Ribeiro Demartini, and Jay J. Thelen, “Global quantitative proteomics using spectral counting: An inexpensive experimental and bioinformatics workflow for deep proteome coverage,” Methods in Molecular Biology, vol. 1072, pp. 171–183, 2014. View at Publisher · View at Google Scholar
  • Arundhathi Sriharshan, Omid Azimzadeh, Randolph B. Caldwell, and Soile Tapio, “Proteomic strategies: SILAC and 2D-DIGE - Powerful tool to investigate cellular alterations,” Methods in Molecular Biology, vol. 1101, pp. 369–392, 2014. View at Publisher · View at Google Scholar
  • Arundhathi Sriharshan, Omid Azimzadeh, Randolph B. Caldwell, and Soile Tapio, “Proteomic strategies: SILAC and 2D-DIGE - Powerful tool to investigate cellular alterations,” Methods in Molecular Biology, vol. 1101, pp. 369–392, 2014. View at Publisher · View at Google Scholar
  • Chun Li, Qi Qiu, Yong Wang, Ping Li, Cheng Xiao, Hongxia Wang, Yang Lin, and Wei Wang, “Time course label-free quantitative analysis of cardiac muscles of rats after myocardial infarction,” Molecular Biosystems, vol. 10, no. 3, pp. 505–513, 2014. View at Publisher · View at Google Scholar
  • Eva Alvarez de Eulate, Liang Qiao, Micheal D. Scanlon, Hubert H. Girault, and Damien W. M. Arrigan, “Fingerprinting the tertiary structure of electroadsorbed lysozyme at soft interfaces by electrostatic spray ionization mass spectrometry,” Chemical Communications, vol. 50, no. 80, pp. 11829–11832, 2014. View at Publisher · View at Google Scholar
  • Gerald W. Hart, and Junfeng Ma, “O-GlcNAc profiling: From proteins to proteomes,” Clinical Proteomics, vol. 11, no. 1, 2014. View at Publisher · View at Google Scholar
  • Oscar Alzate, Cristina Osorio, Robert M. DeKroon, Ana Corcimaru, and Harsha P. Gunawardena, “Differentially charged isoforms of apolipoprotein E from human blood are potential biomarkers of Alzheimer's disease,” Alzheimers Research & Therapy, vol. 6, no. 4, 2014. View at Publisher · View at Google Scholar
  • Chaochao Wu, Tao Liu, Erin S. Baker, Karin D. Rodland, and Richard D. Smithvol. 1-2, pp. 17–48, 2015. View at Publisher · View at Google Scholar
  • Marta Gallego, Leticia Mora, M. Concepción Aristoy, and Fidel Toldrá, “The use of label-free mass spectrometry for relative quantification of sarcoplasmic proteins during the processing of dry-cured ham,” Food Chemistry, 2015. View at Publisher · View at Google Scholar
  • Solmaz Khaghani-Razi-Abad, Mehrdad Hashemi, Mehdi Pooladi, Maliheh Entezari, and Elham Kazemi, “Proteomics analysis of human oligodendroglioma proteome,” Gene, vol. 569, no. 1, pp. 77–82, 2015. View at Publisher · View at Google Scholar
  • Evelyne Maes, Inge Mertens, Dirk Valkenborg, Patrick Pauwels, Christian Rolfo, and Geert Baggerman, “Proteomics in cancer research: Are we ready for clinical practice?,” Critical Reviews in Oncology/Hematology, 2015. View at Publisher · View at Google Scholar
  • I. Iovinella, B. Caputo, E. Michelucci, F.R. Dani, and A. della Torre, “Candidate biomarkers for mosquito age-grading identified by label-free quantitative analysis of protein expression in Aedes albopictus females,” Journal of Proteomics, 2015. View at Publisher · View at Google Scholar
  • Avik Basu, Sandra Harper, Esther N. Pesciotta, Kaye D. Speicher, Abhijit Chakrabarti, and David W. Speicher, “Proteome Analysis of the Triton-Insoluble Erythrocyte Membrane Skeleton,” Journal of Proteomics, 2015. View at Publisher · View at Google Scholar
  • Seung Yun Yim, Eunjung Ryu, Jae-Young Lim, Eun Joo Yang, and Seung-Min Lee, “Serum fibronectin 1 and ApoE levels increase with risk of lymphedema in Korean breast cancer survivors,” Supportive Care In Cancer, vol. 23, no. 8, pp. 2319–2326, 2015. View at Publisher · View at Google Scholar
  • James A Madsen, Victor Farutin, Theresa Carbeau, Steve Wudyka, Yan Yin, Stephen Smith, James Anderson, and Ishan Capila, “Toward the complete characterization of host cell proteins in biotherapeutics via affinity depletions, LC-MS/MS, and multivariate analysis,” mAbs, pp. 1–10, 2015. View at Publisher · View at Google Scholar
  • Feng Li, Feng-Yong Yang, Xue-Jun Wei, and Chong-Hao Duan, “Retracted Article: Serum protein biomarkers screening in patients with ischemic stroke by LC-MS/MS,” International Journal of Neuroscience, vol. 126, no. 8, pp. 692–699, 2015. View at Publisher · View at Google Scholar
  • Xue-jun Wei, Feng Li, Feng-yong Yang, and Chong-hao Duan, “Serum protein biomarkers screening in patients with ischemic stroke by LC-MS/MS,” International Journal of Neuroscience, pp. 1–8, 2015. View at Publisher · View at Google Scholar
  • Albert-Baskar Arul, Munkhtsolmon Byambadorj, Na-Young Han, Jong Moon Park, and Hookeun Lee, “Development of an Automated, High-throughput Sample Preparation Protocol for Proteomics Analysis,” Bulletin Of The Korean Chemical Society, vol. 36, no. 7, pp. 1791–1798, 2015. View at Publisher · View at Google Scholar
  • Gerhard Mayer, Christian Stephan, Helmut E. Meyer, Michael Kohl, Katrin Marcus, and Martin Eisenacher, “ProCon – PROteomics CONversion tool,” Journal of Proteomics, 2015. View at Publisher · View at Google Scholar
  • Shweta Fulsundar, Heramb M. Kulkarni, Medicharla V. Jagannadham, Rashmi Nair, Sravani Keerthi, Pooja Sant, Karishma Pardesi, Jayesh Bellare, and Balu Ananda Chopade, “Molecular characterization of outer membrane vesicles released from Acinetobacter radioresistens and their potential roles in pathogenesis,” Microbial Pathogenesis, 2015. View at Publisher · View at Google Scholar
  • Chanida Puangpila, and Ziad El Rassi, “Capturing and identification of differentially expressed fucome by a gel free and label free approach,” Journal Of Chromatography B-Analytical Technologies In The Biomedical And Life Sciences, vol. 989, pp. 112–121, 2015. View at Publisher · View at Google Scholar
  • Hongyan Zhang, and Ren'an Wu, “Proteomic profiling of protein corona formed on the surface of nanomaterial,” Science China-Chemistry, vol. 58, no. 5, pp. 780–792, 2015. View at Publisher · View at Google Scholar
  • Lawrence W. Dick, John T. Mehl, John W. Loughney, Anna Mach, Richard R. Rustandi, Sha Ha, Lan Zhang, Craig T. Przysiecki, Lance Dieter, and Van M. Hoang, “Label-free quantitative mass spectrometry for analysis of protein antigens in a meningococcal group b outer membrane vesicle vaccine,” Human Vaccines & Immunotherapeutics, pp. 00–00, 2015. View at Publisher · View at Google Scholar
  • S. Y. Kim, J-W Theunissen, J. Balibalos, S. Liao-Chan, M. C. Babcock, T. Wong, B. Cairns, D. Gonzalez, E. H. van der Horst, M. Perez, Z. Levashova, L. Chinn, J. A. D'Alessio, M. Flory, A. Bermudez, D. Y. Jackson, E. Ha, J. Monteon, M. F. Bruhns, G. Chen, and T-S Migone, “A novel antibody-drug conjugate targeting SAIL for the treatment of hematologic malignancies,” Blood Cancer Journal, vol. 5, 2015. View at Publisher · View at Google Scholar
  • Sacha K. Stelder, Siraje A. Mahmud, Henk L. Dekker, Leo J. De Koning, Stanley Brul, and Chris G. De Koster, “Temperature dependence of the proteome profile of the psychrotolerant pathogenic food spoiler bacillus weihenstephanensis type strain WSBC 10204,” Journal of Proteome Research, vol. 14, no. 5, pp. 2169–2176, 2015. View at Publisher · View at Google Scholar
  • Caroline Marcon, Waqas Ahmed Malik, Justin W. Walley, Zhouxin Shen, Anja Paschold, Laurie G. Smith, Hans-Peter Piepho, Steven P. Briggs, and Frank Hochholdinger, “A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes,” Plant Physiology, vol. 168, no. 1, pp. 233–U430, 2015. View at Publisher · View at Google Scholar
  • Christopher R. Dunston, Rebecca Herbert, and Helen R. Griffiths, “Improving T cell- induced response to subunit vaccines: opportunities for a proteomic systems approach,” Journal Of Pharmacy And Pharmacology, vol. 67, no. 3, pp. 290–299, 2015. View at Publisher · View at Google Scholar
  • Jesus V. Jorrin-Novo, Jesus Pascual, Rosa Sanchez-Lucas, M. Cristina Romero-Rodriguez, Manuel J. Rodriguez-Ortega, Christof Lenz, and Luis Valledor, “Fourteen years of plant proteomics reflected in Proteomics: Moving from model species and 2DE-based approaches to orphan species and gel-free platform,” Proteomics, vol. 15, no. 5-6, pp. 1089–1112, 2015. View at Publisher · View at Google Scholar
  • Xianping Fang, Jianping Chen, Liangying Dai, Huasheng Ma, Hengmu Zhang, Jian Yang, Fang Wang, and Chengqi Yan, “Proteomic dissection of plant responses to various pathogens,” Proteomics, 2015. View at Publisher · View at Google Scholar
  • Gabriella Pocsfalvi, Christopher Stanly, Annalisa Vilasi, Immacolata Fiume, Giovambattista Capasso, Lilla Turiák, Edit I Buzas, and Károly Vékey, “Mass spectrometry of extracellular vesicles,” Mass Spectrometry Reviews, 2015. View at Publisher · View at Google Scholar
  • Marta Gallego, Leticia Mora, M. Concepción Aristoy, and Fidel Toldrá, “Optimisation of a simple and reliable label-free methodology for the relative quantitation of raw pork meat proteins,” Food Chemistry, 2015. View at Publisher · View at Google Scholar
  • Bridget Calder, Nelson C Soares, Elise de Kock, and Jonathan M Blackburn, “Mycobacterial proteomics: analysis of expressed proteomes and post-translational modifications to identify candidate virulence factors,” Expert Review of Proteomics, vol. 12, no. 1, pp. 21–35, 2015. View at Publisher · View at Google Scholar
  • Anjana Shenoy, and Tamar Geiger, “Super-SILAC: current trends and future perspectives,” Expert Review of Proteomics, vol. 12, no. 1, pp. 13–19, 2015. View at Publisher · View at Google Scholar
  • Yu-Ning Wei, Hai-Yang Hu, Gang-Cai Xie, Ning Fu, Zhi-Bin Ning, Rong Zeng, and Philipp Khaitovich, “Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging,” Genome Biology, vol. 16, 2015. View at Publisher · View at Google Scholar
  • Hui Wang, Tujin Shi, Wei-Jun Qian, Tao Liu, Jacob Kagan, Sudhir Srivastava, Richard D. Smith, Karin D. Rodland, and David G. Camp, “The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification,” Expert Review of Proteomics, vol. 13, no. 1, pp. 99–114, 2015. View at Publisher · View at Google Scholar
  • Fei Ye, Zhongshuai Xin, Wei Han, Jingjing Fan, Bin Yin, Shuzhen Wu, Wei Yang, Jiangang Yuan, Boqin Qiang, Wei Sun, and Xiaozhong Peng, “Quantitative Proteomics Analysis of the Hepatitis C Virus Replicon High-Permissive and Low-Permissive Cell Lines,” PLoS One, vol. 10, no. 11, 2015. View at Publisher · View at Google Scholar
  • Hannah Johnson, “Uncovering dynamic phosphorylation signaling using mass spectrometry,” International Journal Of Mass Spectrometry, vol. 391, pp. 123–138, 2015. View at Publisher · View at Google Scholar
  • Roland F. Rivera-Santiago, Sira Sriswasdi, Sandra L. Harper, and David W. Speicher, “Probing structures of large protein complexes using zero-length cross-linking,” Methods, vol. 89, pp. 99–111, 2015. View at Publisher · View at Google Scholar
  • Xiaomeng Shen, Qiang Hu, Jun Li, Jianmin Wang, and Jun Qu, “Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics,” Journal Of Proteome Research, vol. 14, no. 10, pp. 4147–4157, 2015. View at Publisher · View at Google Scholar
  • Pan Chao, Su Yun-Cong, Yang Rui, Duan Hui-Long, and Deng Ning, “A Mass Spectrometry-based Label-free Quantitative Approach Coupled With Complex Proteome Functional Analysis,” Progress In Biochemistry And Biophysics, vol. 42, no. 1, pp. 82–90, 2015. View at Publisher · View at Google Scholar
  • Caroline Marcon, Waqas Ahmed Malik, Justin W. Walley, Zhouxin Shen, Anja Paschold, Laurie G. Smith, Hans-Peter Piepho, Steven P. Briggs, and Frank Hochholdinger, “A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes,” Plant Physiology, vol. 168, no. 1, pp. 233–246, 2015. View at Publisher · View at Google Scholar
  • Satwinderjeet Kaur, Jasmine George, Nihal Ahmad, Chandra K. Singh, Minakshi Nihal, Molly C. Pellitteri Hahn, and Cameron O. Scarlett, “Molecular signatures of sanguinarine in human pancreatic cancer cells: A large scale label-free comparative proteomics approach,” Oncotarget, vol. 6, no. 12, pp. 10335–10349, 2015. View at Publisher · View at Google Scholar
  • Yanuar Alan Sulistio, and Klaus Heese, “Proteomics in Traditional Chinese Medicine with an Emphasis on Alzheimer’s Disease,” Evidence-Based Complementary and Alternative Medicine, vol. 2015, pp. 1–17, 2015. View at Publisher · View at Google Scholar
  • Qidi Ai, Guibo Sun, Yun Luo, Xi Dong, Ruifeng Hu, Xiangbao Meng, and Xiaobo Sun, “Ginsenoside Rb1 prevents hypoxia-reoxygenation-induced apoptosis in H9c2 cardiomyocytes via an estrogen receptor-dependent crosstalk among the Akt, JNK, and ERK 1/2 pathways using a label-free quantitative proteomics analysis,” RSC Adv., vol. 5, no. 33, pp. 26346–26363, 2015. View at Publisher · View at Google Scholar
  • Dana Flodrova, Dagmar Benkovska, Marketa Lastovickova, and Janette Bobalova, “HPLC Bottom-Up MS-Based Proteomics for Mapping of Specific Proteins in Several European Spring Barley Varieties,” Journal Of The American Society Of Brewing Chemists, vol. 73, no. 1, pp. 71–77, 2015. View at Publisher · View at Google Scholar
  • Bhardwaj Gourav, Marcus Dörr, Praveen Kumar Sappa, Sabine Ameling, Vishnu Dhople, Leif Steil, Karin Klingel, Klaus Empen, Daniel Beug, Uwe Völker, Stephan B. Felix, and Elke Hammer, “Endomyocardial proteomic signature corresponding to the response of patients with dilated cardiomyopathy to immunoadsorption therapy,” Journal of Proteomics, 2016. View at Publisher · View at Google Scholar
  • Leticia Mora, Fidel Toldrá, and Marta Gallego, “Peptidomics as a tool for quality control in dry-cured ham processing,” Journal of Proteomics, vol. 147, pp. 98–107, 2016. View at Publisher · View at Google Scholar
  • Zhenqi Zhou, Jianhong Zhou, Yuchun Du, and Ahmed E. Dhamad, “Systematic proteomic identification of the heat shock proteins (Hsp) that interact with estrogen receptor alpha (ERα) and biochemical characterization of the ERα-Hsp70 interaction,” PLoS ONE, vol. 11, no. 8, 2016. View at Publisher · View at Google Scholar
  • Junying Wei, Chen Ding, Yanqiong Zhang, Defeng Li, Lei Song, Yanzhen Hu, Hongjun Yang, Luqi Huang, Qiang Jia, Mingwei Liu, Yi Zhang, and Minghua Xian, “Systematic investigation of transcription factors critical in the protection against cerebral ischemia by Danhong injection,” Scientific Reports, vol. 6, 2016. View at Publisher · View at Google Scholar
  • Éva Csősz, Eszter Deák, Gergő Kalló, Adrienne Csutak, and József Tőzsér, “Diabetic retinopathy: Proteomic approaches to help the differential diagnosis and to understand the underlying molecular mechanisms,” Journal of Proteomics, 2016. View at Publisher · View at Google Scholar
  • John R. Yates, Yvonne S. Ziegler, James J. Moresco, and Ann M. Nardulli, “Integration of breast cancer secretomes with clinical data elucidates potential serum markers for disease detection, diagnosis, and prognosis,” PLoS ONE, vol. 11, no. 6, 2016. View at Publisher · View at Google Scholar
  • Luca Pandolfini, Ettore Luzi, Dario Bressan, Nadia Ucciferri, Michele Bertacchi, Rossella Brandi, Silvia Rocchiccioli, Mara D'Onofrio, and Federico Cremisi, “RISC-mediated control of selected chromatin regulators stabilizes ground state pluripotency of mouse embryonic stem cells,” Genome Biology, vol. 17, 2016. View at Publisher · View at Google Scholar
  • Wishwas Abhyankar, Sacha Stelder, Leo de Koning, Chris de Koster, and Stanley Brul, “‘Omics’ for microbial food stability: Proteomics for the development of predictive models for bacterial spore stress survival and outgrowth,” International Journal of Food Microbiology, 2016. View at Publisher · View at Google Scholar
  • Hung Tiong, Steven Hartson, and Peter Muriana, “Comparison of Surface Proteomes of Adherence Variants of Listeria Monocytogenes Using LC-MS/MS for Identification of Potential Surface Adhesins,” Pathogens, vol. 5, no. 2, pp. 40, 2016. View at Publisher · View at Google Scholar
  • Vaibhav Srivastava, Joseph R. Weber, Erik Malm, Bruce W. Fouke, and Vincent Bulone, “Proteomic Analysis of a Poplar Cell Suspension Culture Suggests a Major Role of Protein S-Acylation in Diverse Cellular Processes,” Frontiers in Plant Science, vol. 7, 2016. View at Publisher · View at Google Scholar
  • Tommaso De Marchi, Rene B. H. Braakman, Christoph Stingl, Martijn M. van Duijn, Marcel Smid, John A. Foekens, Theo M. Luider, John W. M. Martens, and Arzu Umar, “The advantage of laser-capture microdissection over whole tissue analysis in proteomic profiling studies,” Proteomics, vol. 16, no. 10, pp. 1474–1485, 2016. View at Publisher · View at Google Scholar
  • Sung Ho Yun, Chi-Won Choi, Sang-Yeop Lee, Edmond Changkyun Park, and Seung Il Kim, “A Proteomics Approach for the Identification of Novel Proteins in Extremophiles,” Biotechnology of Extremophiles:, vol. 1, pp. 303–319, 2016. View at Publisher · View at Google Scholar
  • Shalini Singh, and Vikash Kumar Dubey, “Quantitative Proteome Analysis of Leishmania donovani under Spermidine Starvation,” Plos One, vol. 11, no. 4, 2016. View at Publisher · View at Google Scholar
  • Orla Coleman, Michael Henry, Gerard McVey, Martin Clynes, Michael Moriarty, and Paula Meleady, “Proteomic strategies in the search for novel pancreatic cancer biomarkers and drug targets: recent advances and clinical impact,” Expert Review of Proteomics, vol. 13, no. 4, pp. 383–394, 2016. View at Publisher · View at Google Scholar
  • Dihong Lu, Weimin Ni, Bruce A. Stanley, and Hong Ma, “Proteomics and transcriptomics analyses of Arabidopsis floral buds uncover important functions of ARABIDOPSIS SKP1-LIKE1,” Bmc Plant Biology, vol. 16, 2016. View at Publisher · View at Google Scholar
  • Liman Zhang, Chen Wu, Gaihong Cai, She Chen, and Keqiong Ye, “Stepwise and dynamic assembly of the earliest precursors of small ribosomal subunits in yeast,” Genes & Development, vol. 30, no. 6, pp. 718–732, 2016. View at Publisher · View at Google Scholar
  • Uzma Urooj Malik, Shamshad Zarina, and Stephen R. Pennington, “Oral squamous cell carcinoma: Key clinical questions, biomarker discovery, and the role of proteomics,” Archives of Oral Biology, vol. 63, pp. 53–65, 2016. View at Publisher · View at Google Scholar
  • Matej Vizovisek, Robert Vidmar, Marko Fonovic, and Boris Turk, “Current trends and challenges in proteomic identification of protease substrates,” Biochimie, vol. 122, pp. 77–87, 2016. View at Publisher · View at Google Scholar
  • Putty-Reddy Sudhir, and Chung-Hsuan Chen, “Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology,” International Journal of Molecular Sciences, vol. 17, no. 3, pp. 432, 2016. View at Publisher · View at Google Scholar
  • Kelly M. Balmant, Tong Zhang, and Sixue Chen, “Protein Phosphorylation and Redox Modification in Stomatal Guard Cells,” Frontiers in Physiology, vol. 7, 2016. View at Publisher · View at Google Scholar
  • Ali Azimi, Kimberley L. Kaufman, Steven Kossard, Marina Ali, and Pablo Fernandez-Penas, “In silico analysis validates proteomic findings of formalin-fixed paraffin embedded cutaneous squamous cell carcinoma tissue,” Cancer Genomics and Proteomics, vol. 13, no. 6, pp. 453–466, 2016. View at Publisher · View at Google Scholar
  • Laura Romas, Kenzie Birse, Kenneth H. Mayer, Max Abou, Garrett Westmacott, Rebecca Giguere, Irma Febo, Ross D. Cranston, Alex Carballo-Diéguez, Ian McGowan, and Adam Burgener, “Rectal 1% Tenofovir Gel Use Associates with Altered Epidermal Protein Expression,” AIDS Research and Human Retroviruses, vol. 32, no. 10-11, pp. 1005–1015, 2016. View at Publisher · View at Google Scholar
  • McKiernan, Legg, and Reisdorphpp. 233–248, 2016. View at Publisher · View at Google Scholar
  • Xiangnan Meng, Haiyan Fan, Na Cui, Juyong Zhao, Kexin Meng, Tiefeng Song, and Yang Yu, “A comparative cell wall proteomic analysis of cucumber leaves under Sphaerotheca fuliginea stress,” Acta Physiologiae Plantarum, vol. 38, no. 11, 2016. View at Publisher · View at Google Scholar
  • Andrew J. Percy, Sarah A. Michaud, Armando Jardim, Nicholas J. Sinclair, Suping Zhang, Yassene Mohammed, Andrea L. Palmer, Darryl B. Hardie, Juncong Yang, Andre M. LeBlanc, and Christoph H. Borchers, “Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue,” Proteomics, 2016. View at Publisher · View at Google Scholar
  • F.G. Teixeira, A. Pires, S.C. Serra, N. Sousa, and A.J. Salgado, “The evolving concept of mesenchymal stromal cells in regenerative medicine,” The Biology and Therapeutic Application of Mesenchymal Cells, pp. 222–235, 2016. View at Publisher · View at Google Scholar
  • Mehdi Mirzaei, Joel M. Chick, Yunqi Wu, Tim Maher, Dana Pascovici, Prathiba Ravishankar, Robert D. Willows, David Handler, Masoud Zabet Moghaddam, Paul A. Haynes, and Ghasem Hosseini Salekdehpp. 1–29, 2016. View at Publisher · View at Google Scholar
  • Tae Kwon Kim, Lucas Tirloni, Antonio F. M. Pinto, James Moresco, John R. Yates, Itabajara da Silva Vaz, and Albert Mulenga, “Ixodes scapularis Tick Saliva Proteins Sequentially Secreted Every 24 h during Blood Feeding,” Plos Neglected Tropical Diseases, vol. 10, no. 1, 2016. View at Publisher · View at Google Scholar
  • Soon-Wook Kwon, Mijeong Kim, Hijin Kim, and Joohyun Lee, “ Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress in Brassica rapa L. (Inbred Line “Chiifu”) ,” International Journal of Genomics, vol. 2016, pp. 1–9, 2016. View at Publisher · View at Google Scholar
  • Esther Imperlini, Lucia Santorelli, Stefania Orrù, Emanuela Scolamiero, Margherita Ruoppolo, and Marianna Caterino, “Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias,” BioMed Research International, vol. 2016, pp. 1–13, 2016. View at Publisher · View at Google Scholar
  • Viktoria M. Enk, Christian Baumann, Michaela Thoß, Kenneth C. Luzynski, Ebrahim Razzazi-Fazeli, and Dustin J. Penn, “Regulation of highly homologous major urinary proteins in house mice quantified with label-free proteomic methods,” Mol. BioSyst., 2016. View at Publisher · View at Google Scholar
  • Manikhandan Mudaliar, Riccardo Tassi, Funmilola C. Thomas, Tom N. McNeilly, Stefan K. Weidt, Mark McLaughlin, David Wilson, Richard Burchmore, Pawel Herzyk, P. David Eckersall, and Ruth N. Zadoks, “Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics,” Mol. BioSyst., 2016. View at Publisher · View at Google Scholar
  • Piotr Stefanowicz, Alicja Kluczyk, and Zbigniew Szewczuk, “Derivatization of peptides for improved detection by mass spectrometry,” Amino Acids, Peptides and Proteins, vol. 40, pp. 36–74, 2016. View at Publisher · View at Google Scholar
  • Malcolm Burns, Gordon Wiseman, Angus Knight, Peter Bramley, Lucy Foster, Sophie Rollinson, Andrew Damant, and Sandy Primrose, “Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud,” Analyst, vol. 141, no. 1, pp. 45–61, 2016. View at Publisher · View at Google Scholar
  • Benedetta Turriziani, Alexander von Kriegsheim, and Stephen R. Pennington, “Protein-protein interaction detection via mass spectrometry-based proteomics,” Advances in Experimental Medicine and Biology, vol. 919, pp. 383–396, 2016. View at Publisher · View at Google Scholar
  • Thibaut Léger, Camille Garcia, Mathieu Videlier, and Jean-Michel Camadro, “Label-free quantitative proteomics in yeast,” Methods in Molecular Biology, vol. 1361, pp. 289–307, 2016. View at Publisher · View at Google Scholar
  • C. Zhang, and Y. Liu, “Retrieving Quantitative Information of Histone PTMs by Mass Spectrometry,” 2016. View at Publisher · View at Google Scholar
  • Josué Delgado, Miguel A. Asensio, Rebecca A. Owens, Sean Doyle, and Félix Núñez, “Quantitative proteomics reveals new insights into calcium-mediated resistance mechanisms in Aspergillus flavus against the antifungal protein PgAFP in cheese,” Food Microbiology, vol. 66, pp. 1–10, 2017. View at Publisher · View at Google Scholar
  • Abidali Mohamedali, Seong Beom Ahn, Alberto Avolio, Nurul Farhana Jufri, and Mark Scott Baker, “Effects of acute and chronic biomechanical strain on human cerebral endothelial cells in altering their proteome profile,” Current Proteomics, vol. 14, no. 3, pp. 214–223, 2017. View at Publisher · View at Google Scholar
  • Anil K Shukla, Vladislav A Petyuk, Nikola Tolić, Ljiljana Paša-Tolić, Richard D Smith, Paul D Piehowski, Christopher Wilkins, Mowei Zhou, Grant M Fujimoto, Yufeng Shen, Jungkap Park, Ronald J Moore, Tao Liu, Samuel H Payne, Sangtae Kim, Joshua Mendoza, Bryson C Gibbons, and Jared B Shaw, “Informed-Proteomics: Open-source software package for top-down proteomics,” Nature Methods, vol. 14, no. 9, pp. 909–914, 2017. View at Publisher · View at Google Scholar
  • Yin-Kwan Wong, Jianbin Zhang, Zi-Chun Hua, Qingsong Lin, Han-Ming Shen, and Jigang Wang, “Recent advances in quantitative and chemical proteomics for autophagy studies,” Autophagy, pp. 1–15, 2017. View at Publisher · View at Google Scholar
  • Jinbao Zhang, Xiaochen Wu, Qin Yue, Weikun Jia, Hui Ouyang, Dong Xin, and Yingbin Xiao, “A novel approach for characterizing variations in serum peptides in rheumatic heart disease,” Indian Journal of Medical Research, vol. 145, no. March, pp. 365–372, 2017. View at Publisher · View at Google Scholar
  • Guilan Di, Hui Li, Chao Zhang, Yanjing Zhao, Chuanjiang Zhou, Sajid Naeem, Li Li, and Xianghui Kong, “Label-free proteomic analysis of intestinal mucosa proteins in common carp (Cyprinus carpio) infected with Aeromonas hydrophila,” Fish and Shellfish Immunology, vol. 66, pp. 11–25, 2017. View at Publisher · View at Google Scholar
  • Gamze Nur Kara, Mustafa Guzel, and Bulent Kabak, “Novel Approaches to Identify and Characterise Microorganisms in Food Industry,” Modern Tools and Techniques to Understand Microbes, pp. 25–43, 2017. View at Publisher · View at Google Scholar
  • Irina A. Tarasova, Mikhail V. Gorshkov, Julia A. Bubis, Lev I. Levitsky, and Mark V. Ivanov, “Comparative evaluation of label-free quantification methods for shotgun proteomics,” Rapid Communications in Mass Spectrometry, vol. 31, no. 7, pp. 606–612, 2017. View at Publisher · View at Google Scholar
  • Moon-Won Yoo, Jisook Park, Hye-Seung Han, Yeo-Min Yun, Jeong Won Kang, Do-Young Choi, Joon won Lee, Jae Hun Jung, Kyung-Yung Lee, and Kwang Pyo Kim, “Discovery of gastric cancer specific biomarkers by the application of serum proteomics,” Proteomics, vol. 17, no. 6, pp. 1600332, 2017. View at Publisher · View at Google Scholar
  • Cristina Banfi, Roberta Baetta, Erica Gianazza, and Elena Tremoli, “Technological advances and proteomic applications in drug discovery and target deconvolution: identification of the pleiotropic effects of statins,” Drug Discovery Today, 2017. View at Publisher · View at Google Scholar
  • Alfredo Oliveros, Phillip Starski, Daniel Lindberg, Sun Choi, Carrie J. Heppelmann, Surendra Dasari, and Doo-Sup Choi, “Label-Free Neuroproteomics of the Hippocampal-Accumbal Circuit Reveals Deficits in Neurotransmitter and Neuropeptide Signaling in Mice Lacking Ethanol-Sensitive Adenosine Transporter,” Journal of Proteome Research, 2017. View at Publisher · View at Google Scholar
  • Victoria Pando-Robles, and Cesar V. Batista, “ Aedes- Borne Virus–Mosquito Interactions: Mass Spectrometry Strategies and Findings ,” Vector-Borne and Zoonotic Diseases, 2017. View at Publisher · View at Google Scholar
  • Javier Soria, Arantxa Acera, Jesús Merayo-LLoves, Juan A. Durán, Nerea González, Sandra Rodriguez, Nikitas Bistolas, Soeren Schumacher, Frank F. Bier, Harald Peter, Walter Stöcklein, and Tatiana Suárez, “Tear proteome analysis in ocular surface diseases using label-free LC-MS/MS and multiplexed-microarray biomarker validation,” Scientific Reports, vol. 7, no. 1, 2017. View at Publisher · View at Google Scholar
  • Raqual Bower, Douglas Tritschler, Kristyn VanderWaal Mills, Thomas Heuser, Daniela Nicastro, and Mary E. Porter, “DRC2/CCDC65 is a central hub for assembly of the nexin–dynein regulatory complex and other regulators of ciliary and flagellar motility,” Molecular Biology of the Cell, vol. 29, no. 2, pp. 137–153, 2017. View at Publisher · View at Google Scholar
  • José Antonio Infantes-Lorenzo, Inmaculada Moreno, María de los Ángeles Risalde, Álvaro Roy, Margarita Villar, Beatriz Romero, Nieves Ibarrola, José de la Fuente, Eugenia Puentes, Lucía de Juan, Christian Gortázar, Javier Bezos, Lucas Domínguez, and Mercedes Domínguez, “Proteomic characterisation of bovine and avian purified protein derivatives and identification of specific antigens for serodiagnosis of bovine tuberculosis,” Clinical Proteomics, vol. 14, no. 1, 2017. View at Publisher · View at Google Scholar
  • Guilan Di, Xianghui Kong, Xiulian Miao, Yifang Zhang, Miaoqin Huang, Yuting Gu, Weiwei You, Jianxin Zhang, and Caihuan Ke, “Proteomic analysis of trochophore and veliger larvae development in the small abalone Haliotis diversicolor.,” BMC genomics, vol. 18, no. 1, pp. 809, 2017. View at Publisher · View at Google Scholar
  • Anna Kupniewska, Krystyna Szymanska, and Urszula Demkow, “Proteomics in the Diagnosis of Inborn Encephalopathies of Unknown Origin: A Myth or Reality,” 2017. View at Publisher · View at Google Scholar
  • Simon R. Hemelaar, Andreas Nagl, François Bigot, Melissa M. Rodríguez-García, Marcel P. de Vries, Mayeul Chipaux, and Romana Schirhagl, “The interaction of fluorescent nanodiamond probes with cellular media,” Microchimica Acta, 2017. View at Publisher · View at Google Scholar
  • Yunqi Wu, Mehdi Mirzaei, and Paul A. Haynes, “Proteomics of Rice—Our Most Valuable Food Crop,” Proteomics in Food Science, pp. 17–33, 2017. View at Publisher · View at Google Scholar
  • Elena Burillo, Inmaculada Jorge, Diego Martínez-López, Emilio Camafeita, Jesus Vazquez, and Jose L. Martin–Ventura, “The Application of Proteomic Techniques in the Study of HDL Particle Characterization and Biomarker Discovery,” The HDL Handbook, pp. 231–255, 2017. View at Publisher · View at Google Scholar
  • Marta Gallego, Leticia Mora, and Fidel Toldrá, “Perspectives in the Use of Peptidomics in Ham,” Proteomics, vol. 18, no. 18, 2018. View at Publisher · View at Google Scholar
  • A. P. Martínez-González, H. D. Ardila, S. T. Martínez-Peralta, L. M. Melgarejo-Muñoz, M. A. Castillejo-Sánchez, and J. V. Jorrín-Novo, “What proteomic analysis of the apoplast tells us about plant-pathogen interactions,” Plant Pathology, 2018. View at Publisher · View at Google Scholar
  • Yirong Zhang, Yawen Chen, Jianqun Zheng, Juan Wang, Shichao Duan, Wei Zhang, Xiumin Yan, and Xueliang Zhu, “Vertebrate Dynein-f depends on Wdr78 for axonemal localization and is essential for ciliary beat,” Journal of Molecular Cell Biology, 2018. View at Publisher · View at Google Scholar
  • Torsten Bohn, Sébastien Planchon, Céline C. Leclercq, Johanna Mihaly, Jenny Renaut, Gabriella Beke, and Ralph Rühl, “Proteomic responses of carotenoid and retinol administration to Mongolian gerbils,” Food and Function, vol. 9, no. 7, pp. 3835–3844, 2018. View at Publisher · View at Google Scholar
  • Yoshiki Nakashima, Saifun Nahar, Chika Miyagi-Shiohira, Takao Kinjo, Naoya Kobayashi, Issei Saitoh, Masami Watanabe, Jiro Fujita, and Hirofumi Noguchi, “A Liquid Chromatography with Tandem Mass Spectrometry-Based Proteomic Analysis of Cells Cultured in DMEM 10% FBS and Chemically Defined Medium Using Human Adipose-Derived Mesenchymal Stem Cells,” International Journal of Molecular Sciences, vol. 19, no. 7, pp. 2042, 2018. View at Publisher · View at Google Scholar
  • Stephen Mackessy, Jamie Leroy, Estrella Mociño-Deloya, Kirk Setser, Robert Bryson, and Anthony Saviola, “Venom Ontogeny in the Mexican Lance-Headed Rattlesnake (Crotalus polystictus),” Toxins, vol. 10, no. 7, pp. 271, 2018. View at Publisher · View at Google Scholar
  • Michiel Bontinck, Jelle Van Leene, Astrid Gadeyne, Bert De Rybel, Dominique Eeckhout, Hilde Nelissen, and Geert De Jaeger, “Recent Trends in Plant Protein Complex Analysis in a Developmental Context,” Frontiers in Plant Science, vol. 9, 2018. View at Publisher · View at Google Scholar
  • Hsin-Pai Li, Chen-Ching Peng, Chih-Ching Wu, Chien-Hsun Chen, Meng-Jhe Shih, Mei-Yuan Huang, Yi-Ru Lai, Yung-Li Chen, Ting-Wen Chen, Petrus Tang, Yu-Sun Chang, Kai-Ping Chang, and Cheng-Lung Hsu, “Inactivation of the tight junction gene CLDN11 by aberrant hypermethylation modulates tubulins polymerization and promotes cell migration in nasopharyngeal carcinoma,” Journal of Experimental & Clinical Cancer Research, vol. 37, no. 1, 2018. View at Publisher · View at Google Scholar
  • Amrita Samanta, Janna Kiselar, Ruth A. Pumroy, Seungil Han, and Vera Y. Moiseenkova-Bell, “Structural insights into the molecular mechanism of mouse TRPA1 activation and inhibition,” The Journal of General Physiology, pp. jgp.201711876, 2018. View at Publisher · View at Google Scholar
  • Sangita Chowdhury-Paul, Victoria Pando-Robles, Verónica Jiménez-Jacinto, Daniel Segura, Guadalupe Espín, and Cinthia Núñez, “Proteomic analysis revealed proteins induced upon Azotobacter vinelandii encystment,” Journal of Proteomics, 2018. View at Publisher · View at Google Scholar
  • Anjana Rustagi, Garvita Singh, Shachi Agrawal, and Prem Kumar Guptapp. 239–264, 2018. View at Publisher · View at Google Scholar
  • Dominique Baiwir, Paolo Nanni, Susanne Müller, Nicolas Smargiasso, Denis Morsa, Edwin De Pauw, and Gabriel Mazzucchelli, “Gel-Free Proteomics,” Proteomics in Domestic Animals: from Farm to Systems Biology, pp. 55–101, 2018. View at Publisher · View at Google Scholar
  • Magdalena Kuras, Lazaro Hiram Betancourt, Melinda Rezeli, Jimmy Rodriguez, Marcell Szasz, Qimin Zhou, Tasso Miliotis, Roland Andersson, and Gyorgy Marko-Varga, “Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks,” Journal of Proteome Research, 2018. View at Publisher · View at Google Scholar
  • Mahalia A. C. Serrano, Jingjing Gao, Katrina A. Kelly, S. Thayumanavan, and Richard W. Vachet, “Supramolecular Polymeric Assemblies for the Selective Depletion of Abundant Acidic Proteins in Serum,” ACS Applied Materials & Interfaces, 2018. View at Publisher · View at Google Scholar
  • Maayan Kaiser, Ryan Arvidson, Raz Zarivach, Michael E. Adams, and Frederic Libersat, “Molecular cross-talk in a unique parasitoid manipulation strategy,” Insect Biochemistry and Molecular Biology, 2018. View at Publisher · View at Google Scholar
  • Natasha Buchs, Sophie Braga-Lagache, Anne-Christine Uldry, Justine Brodard, Christophe Debonneville, Jean-Sébastien Reynard, and Manfred Heller, “Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by Proteomics,” Frontiers in Plant Science, vol. 9, 2018. View at Publisher · View at Google Scholar
  • Saifun Nahar, Yoshiki Nakashima, Chika Miyagi-Shiohira, Takao Kinjo, Naoya Kobayashi, Issei Saitoh, Masami Watanabe, Hirofumi Noguchi, and Jiro Fujita, “A Comparison of Proteins Expressed between Human and Mouse Adipose-Derived Mesenchymal Stem Cells by a Proteome Analysis through Liquid Chromatography with Tandem Mass Spectrometry,” International Journal of Molecular Sciences, vol. 19, no. 11, pp. 3497, 2018. View at Publisher · View at Google Scholar
  • Catharina Keßler, Jan H. Forth, Günther M. Keil, Thomas C. Mettenleiter, Sandra Blome, and Axel Karger, “The intracellular proteome of African swine fever virus,” Scientific Reports, vol. 8, no. 1, 2018. View at Publisher · View at Google Scholar
  • Merry L. Lindsey, Mira Jung, Michael E. Hall, and Kristine Y. DeLeon-Pennell, “Proteomic analysis of the cardiac extracellular matrix: clinical research applications,” Expert Review of Proteomics, pp. 1–8, 2018. View at Publisher · View at Google Scholar
  • Minting Yuan, Pei-Jing Pai, Xiaofen Liu, Henry Lam, and Barbara P. Chan, “Proteomic Analysis of Nucleus Pulposus Cell-derived Extracellular Matrix Niche and Its Effect on Phenotypic Alteration of Dermal Fibroblasts,” Scientific Reports, vol. 8, no. 1, 2018. View at Publisher · View at Google Scholar
  • Dwight R. Causey, David A. Stead, Samuel A.M. Martin, Robert H. Devlin, Daniel J. Macqueen, and Jin-Hyoung Kim, “Proteomic comparison of selective breeding and growth hormone transgenesis in fish: Unique pathways to enhanced growth,” Journal of Proteomics, 2018. View at Publisher · View at Google Scholar
  • Andreas E. Zautner, Wolfgang Bohne, Christof Lenz, Wycliffe O. Masanta, Raimond Lugert, Uwe Gross, Andreas Leha, and Mohammed Dakna, “Proteome Profiling by Label-Free Mass Spectrometry Reveals Differentiated Response of Campylobacter jejuni 81–176 to Sublethal Concentrations of Bile Acids,” Proteomics - Clinical Applications, 2018. View at Publisher · View at Google Scholar
  • Jinping Zhao, Jingjing Xu, Binghua Chen, Weijun Cui, Zhongjing Zhou, Xijiao Song, Zhuo Chen, Hongying Zheng, Lin Lin, Jiejun Peng, Yuwen Lu, Zhiping Deng, Jianping Chen, and Fei Yan, “Characterization of Proteins Involved in Chloroplast Targeting Disturbed by Rice Stripe Virus by Novel Protoplast–Chloroplast Proteomics,” International Journal of Molecular Sciences, vol. 20, no. 2, pp. 253, 2019. View at Publisher · View at Google Scholar