In-depth characterisation of the lamb meat proteome from longissimus lumborum

Bax, 2013, Muscle composition slightly affects in vitro digestion of aged and cooked meat: identification of associated proteomic markers, Food Chem, 136, 1249, 10.1016/j.foodchem.2012.09.049 Xiong, 2004, Chemical and physical characteristics of meat/protein functionality, 218 Morton, 1999, Calpain–calpastatin and toughness in M. longissimus from electrically stimulated lamb and beef carcasses, Meat Sci, 52, 71, 10.1016/S0309-1740(98)00150-8 Sayd, 2006, Proteome analysis of the sarcoplasmic fraction of pig semimembranosus muscle: implications on meat color development, J Agric Food Chem, 54, 2732, 10.1021/jf052569v Joseph, 2012, Proteomics of muscle-specific beef color stability, J Agric Food Chem, 60, 3196, 10.1021/jf204188v Hollung, 2007, Application of proteomics to understand the molecular mechanisms behind meat quality, Meat Sci, 77, 97, 10.1016/j.meatsci.2007.03.018 Montowska, 2013, Species-specific expression of various proteins in meat tissue: proteomic analysis of raw and cooked meat and meat products made from beef, pork and selected poultry species, Food Chem, 136, 1461, 10.1016/j.foodchem.2012.09.072 Picard, 2010, Skeletal muscle proteomics in livestock production, Brief Funct Genomics, 9, 259, 10.1093/bfgp/elq005 Bendixen, 2005, The use of proteomics in meat science, Meat Sci, 71, 138, 10.1016/j.meatsci.2005.03.013 Paredi, 2012, Muscle to meat molecular events and technological transformations: the proteomics insight, J Proteomics, 75, 4275, 10.1016/j.jprot.2012.04.011 Polati, 2012, Proteomic changes involved in tenderization of bovine Longissimus dorsi muscle during prolonged ageing, Food Chem, 135, 2052, 10.1016/j.foodchem.2012.06.093 D’Alessandro, 2013, Meat science: from proteomics to integrated omics towards system biology, J Proteomics, 78, 558, 10.1016/j.jprot.2012.10.023 Wu, 2014, LC MS/MS identification of large structural proteins from bull muscle and their degradation products during post mortem storage, Food Chem, 150, 137, 10.1016/j.foodchem.2013.10.158 Mullen, 2006, Understanding meat quality through the application of genomic and proteomic approaches, Meat Sci, 74, 3, 10.1016/j.meatsci.2006.04.015 Théron, 2011, Proteomic analysis of semimembranosus and biceps femoris muscles from Bayonne dry-cured ham, Meat Sci, 88, 82, 10.1016/j.meatsci.2010.12.006 Škrlep, 2011, Proteomic profile of dry-cured ham relative to PRKAG3 or CAST genotype, level of salt and pastiness, Meat Sci, 88, 657, 10.1016/j.meatsci.2011.02.025 GIRA, 2012 Ledgard, 2011, Carbon footprinting of New Zealand lamb from the perspective of an exporting nation, Anim Front, 1, 40, 10.2527/af.2011-0010 2013 Hamelin, 2006, Proteomic analysis of ovine muscle hypertrophy, J Anim Sci, 84, 3266, 10.2527/jas.2006-162 Hamelin, 2007, Differential expression of sarcoplasmic proteins in four heterogeneous ovine skeletal muscles, Proteomics, 7, 271, 10.1002/pmic.200600309 McDonagh, 2006, Variation in protein abundance profiles in the M. semitendinosus of lambs bred from sires selected on the basis of growth and muscling potential, Aust J Agric Res, 57, 671, 10.1071/AR04277 Zhu, 2006, Maternal nutrient restriction affects properties of skeletal muscle in offspring, J Physiol (Lond), 575, 241, 10.1113/jphysiol.2006.112110 Addis, 2009, Generation of high-quality protein extracts from formalin-fixed, paraffin-embedded tissues, Proteomics, 9, 3815, 10.1002/pmic.200800971 Addis, 2009, 2-D PAGE and MS analysis of proteins from formalin-fixed, paraffin-embedded tissues, Proteomics, 9, 4329, 10.1002/pmic.200900010 de Almeida, 2012, Muscle proteomics profiles in sheep: the effect of breed and nutritional status, 126 Paredi, 2013, Muscle and meat. New horizons and applications for proteomics on a farm to fork perspective, J Proteomics, 88, 58, 10.1016/j.jprot.2013.01.029 Di Luca, 2013, 2D DIGE proteomic analysis of early post mortem muscle exudate highlights the importance of the stress response for improved water-holding capacity of fresh pork meat, Proteomics, 13, 1528, 10.1002/pmic.201200145 Santos, 2013, Mapping sea urchins tube feet proteome – a unique hydraulic mechano-sensory adhesive organ, J Proteomics, 79, 100, 10.1016/j.jprot.2012.12.004 Højlund, 2008, Characterization of the human skeletal muscle proteome by one-dimensional gel electrophoresis and HPLC-ESI-MS/MS, Mol Cell Proteomics, 7, 257, 10.1074/mcp.M700304-MCP200 Parker, 2009, Characterization of human skeletal muscle biopsy samples using shotgun proteomics, J Proteome Res, 8, 3265, 10.1021/pr800873q Bouley, 2004, Mapping of bovine skeletal muscle proteins using two-dimensional gel electrophoresis and mass spectrometry, Proteomics, 4, 1811, 10.1002/pmic.200300688 Chaze, 2006, Mapping of alkaline proteins in bovine skeletal muscle, Proteomics, 6, 2571, 10.1002/pmic.200500452 Talamo, 2003, Proteins from bovine tissues and biological fluids: defining a reference electrophoresis map for liver, kidney, muscle, plasma and red blood cells, Proteomics, 3, 440, 10.1002/pmic.200390059 Hakimov, 2009, Application of iTRAQ to catalogue the skeletal muscle proteome in pigs and assessment of effects of gender and diet dephytinization, Proteomics, 9, 4000, 10.1002/pmic.200900049 Huang, 2011, Gel-based phosphoproteomics analysis of sarcoplasmic proteins in postmortem porcine muscle with pH decline rate and time differences, Proteomics, 11, 4063, 10.1002/pmic.201100173 Almeida, 2009, Establishment of a proteomic reference map for the gastrocnemius muscle in the rabbit (Oryctolagus cuniculus), Res Vet Sci, 87, 196, 10.1016/j.rvsc.2009.02.011 Liu, 2013, Shotgun proteomic analysis of sarcoplasmic reticulum preparations from rabbit skeletal muscle, Proteomics, 13, 2335, 10.1002/pmic.201200138 Raddatz, 2008, A proteome map of murine heart and skeletal muscle, Proteomics, 8, 1885, 10.1002/pmic.200700902 Rayavarapu, 2013, Identification of disease specific pathways using in vivo SILAC proteomics in dystrophin deficient MDX mouse, Mol Cell Proteomics, 12, 1061, 10.1074/mcp.M112.023127 Geiger, 2013, Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse, Mol Cell Proteomics, 12, 1709, 10.1074/mcp.M112.024919 Drexler, 2012, On marathons and sprints: an integrated quantitative proteomics and transcriptomics analysis of differences between slow and fast muscle fibers, Mol Cell Proteomics, 11, 10.1074/mcp.M111.010801 Gebriel, 2010, Cod (Gadus morhua) muscle proteome cataloging using 1D-PAGE protein separation, nano-liquid chromatography peptide fractionation, and linear trap quadrupole (LTQ) mass spectrometry, J Agric Food Chem, 58, 12307, 10.1021/jf103009r Candiano, 2004, Blue silver: a very sensitive colloidal Coomassie G-250 staining for proteome analysis, Electrophoresis, 25, 1327, 10.1002/elps.200305844 Yu, 2015, Data for an in-depth characterisation of the lamb meat proteome from longissimus lumborum, Data Brief, 10.1016/j.dib.2015.02.006 Deb-Choudhury, 2010, Electrophoretic mapping of highly homologous keratins: a novel marker peptide approach, Electrophoresis, 31, 2894, 10.1002/elps.201000134 Naba, 2012, The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices, Mol Cell Proteomics, 11, 10.1074/mcp.M111.014647 Dicker, 2010, Increased power for the analysis of label-free LC–MS/MS proteomics data by combining spectral counts and peptide peak attributes, Mol Cell Proteomics, 9, 2704, 10.1074/mcp.M110.002774 Rappsilber, 2007, Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips, Nat Protoc, 2, 1896, 10.1038/nprot.2007.261 Clerens, 2010, Developing the wool proteome, J Proteomics, 73, 1722, 10.1016/j.jprot.2010.05.005 Archibald, 2010, The sheep genome reference sequence: a work in progress, Anim Genet, 41, 449, 10.1111/j.1365-2052.2010.02100.x Käll, 2007, Semi-supervised learning for peptide identification from shotgun proteomics datasets, Nat Methods, 4, 923, 10.1038/nmeth1113 Brosch, 2009, Accurate and sensitive peptide identification with mascot percolator, J Proteome Res, 8, 3176, 10.1021/pr800982s Käll, 2008, Posterior error probabilities and false discovery rates: two sides of the same coin, J Proteome Res, 7, 40, 10.1021/pr700739d Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, 22, 4673, 10.1093/nar/22.22.4673 Li, 2006, CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658, 10.1093/bioinformatics/btl158 Fu, 2012, CD-HIT: accelerated for clustering the next-generation sequencing data, Bioinformatics, 28, 3150, 10.1093/bioinformatics/bts565 Wu, 2003, The protein information resource, Nucleic Acids Res, 31, 345, 10.1093/nar/gkg040 McGarvey, 2011, Protein-centric data integration for functional analysis of comparative proteomics data, Methods Mol Biol (Clifton, NJ), 694, 323, 10.1007/978-1-60761-977-2_20 Louie, 2009, A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions, PLoS ONE, 4, e7546, 10.1371/journal.pone.0007546 Joshi, 2007, Quantitative assessment of relationship between sequence similarity and function similarity, BMC Genomics, 8, 222, 10.1186/1471-2164-8-222 Binns, 2009, QuickGO: a web-based tool for Gene Ontology searching, Bioinformatics, 25, 3045, 10.1093/bioinformatics/btp536 Wilson, 2009, SUPERFAMILY – sophisticated comparative genomics, data mining, visualization and phylogeny, Nucleic Acids Res, 37, D380, 10.1093/nar/gkn762 Gough, 2001, Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure, J Mol Biol, 313, 903, 10.1006/jmbi.2001.5080 Zdobnov, 2001, InterProScan – an integration platform for the signature-recognition methods in InterPro, Bioinformatics, 17, 847, 10.1093/bioinformatics/17.9.847 Goujon, 2010, A new bioinformatics analysis tools framework at EMBL–EBI, Nucleic Acids Res, 38, W695, 10.1093/nar/gkq313 Lametsch, 2011, Postmortem changes in pork muscle protein phosphorylation in relation to the RN genotype, J Agric Food Chem, 59, 11608, 10.1021/jf201936h Kontrogianni-Konstantopoulos, 2009, Muscle giants: molecular scaffolds in sarcomerogenesis, Physiol Rev, 89, 1217, 10.1152/physrev.00017.2009 Watanabe, 1996, Effect of meat ultimate pH on rate of titin and nebulin degradation, Meat Sci, 42, 407, 10.1016/0309-1740(95)00050-X Young, 2001, Obscurin, a giant sarcomeric Rho guanine nucleotide exchange factor protein involved in sarcomere assembly, J Cell Biol, 154, 123, 10.1083/jcb.200102110 Lange, 2009, Obscurin determines the architecture of the longitudinal sarcoplasmic reticulum, J Cell Sci, 122, 2640, 10.1242/jcs.046193 Clark, 2002, Striated muscle cytoarchitecture: an intricate web of form and function, Annu Rev Cell Dev, 637, 10.1146/annurev.cellbio.18.012502.105840 Gautel, 2011, The sarcomeric cytoskeleton: who picks up the strain, Curr Opin Cell Biol, 23, 39, 10.1016/j.ceb.2010.12.001 Huff Lonergan, 2010, Biochemistry of postmortem muscle – lessons on mechanisms of meat tenderization, Meat Sci, 86, 184, 10.1016/j.meatsci.2010.05.004 Ohlendieck, 2010, Proteomics of skeletal muscle glycolysis, Biochim Biophys Acta (BBA) – Prot Proteomics, 1804, 2089, 10.1016/j.bbapap.2010.08.001 Roberts, 1988, Regulation of binding of phosphofructokinase to myofibrils in the red and white muscle of the barred sand bass, Paralabrax nebulifer (Serranidae), J Exp Biol, 137, 13, 10.1242/jeb.137.1.13 Lametsch, 2002, Identification of protein degradation during post-mortem storage of pig meat, J Agric Food Chem, 50, 5508, 10.1021/jf025555n Wu, 2014, LC MS/MS identification of large structural proteins from bull muscle and their degradation products during post mortem storage, Food Chem, 150, 137, 10.1016/j.foodchem.2013.10.158 Bernevic, 2011, Degradation and oxidation postmortem of myofibrillar proteins in porcine skeleton muscle revealed by high resolution mass spectrometric proteome analysis, Int J Mass Spectrom, 305, 217, 10.1016/j.ijms.2010.11.010 Promeyrat, 2011, Early post-mortem sarcoplasmic proteome of porcine muscle related to protein oxidation, Food Chem, 127, 1097, 10.1016/j.foodchem.2011.01.108 1990, Recommended terminology for the muscle commonly designated ‘longissimus dorsi’, Meat Sci, 28, 259, 10.1016/0309-1740(90)90010-4 Bjarnadóttir, 2012, Changes in protein abundance between tender and tough meat from bovine Longissimus thoracis muscle assessed by isobaric Tag for Relative and Absolute Quantitation (iTRAQ) and 2-dimensional gel electrophoresis analysis, J Anim Sci, 90, 2035, 10.2527/jas.2011-4721 Huang, 2014, Quantitative phosphoproteomic analysis of porcine muscle within 24h postmortem, J Proteomics, 106, 125, 10.1016/j.jprot.2014.04.020 Hornshøj, 2009, Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies, BMC Genomics, 10, 30, 10.1186/1471-2164-10-30 Chen, 2013, Proteome analysis of silkworm, Bombyx mori, larval gonads: characterization of proteins involved in sexual dimorphism and gametogenesis, J Proteome Res, 12, 2422, 10.1021/pr300920z Schirmer, 2003, Nuclear membrane proteins with potential disease links found by subtractive proteomics, Science, 301, 1380, 10.1126/science.1088176 Nesvizhskii, 2005, Interpretation of shotgun proteomic data: the protein inference problem, Mol Cell Proteomics, 4, 1419, 10.1074/mcp.R500012-MCP200 Gupta, 2009, False discovery rates of protein identifications: a strike against the two-peptide rule, J Proteome Res, 8, 4173, 10.1021/pr9004794 Brosch, 2011, Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and resurrected pseudogenes in the mouse genome, Genome Res, 21, 756, 10.1101/gr.114272.110 NCBI, The NCBI eukaryotic genome annotation pipeline, from http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/ Punta, 2008, The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function, PLoS Comput Biol, 4, e1000160, 10.1371/journal.pcbi.1000160 Clark, 2011, Analysis of protein function and its prediction from amino acid sequence, Proteins, 79, 2086, 10.1002/prot.23029