⿿Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples

Bennike, 2014, Biomarkers in inflammatory bowel diseases: current status and proteomics identification strategies, World J. Gastroenterol. WJG, 20, 3231, 10.3748/wjg.v20.i12.3231 Tanca, 2014, Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: insights from liver tissue, Clin. Proteomics, 11, 28, 10.1186/1559-0275-11-28 Steiner, 2014, Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues, Proteomics, 14, 441, 10.1002/pmic.201300311 Espina, 2008, A portrait of tissue phosphoprotein stability in the clinical tissue procurement process, Mol. Cell. Proteomics, 7, 1998, 10.1074/mcp.M700596-MCP200 van Eijsden, 2013, A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study, Biotechnol. Lett., 35, 891, 10.1007/s10529-013-1163-0 Drakulovski, 2013, Use of RNAlater® as a preservation method for parasitic coprology studies in wild-living chimpanzees, Exp. Parasitol., 135, 257, 10.1016/j.exppara.2013.07.002 Abbaraju, 2011, Protein recovery and identification from the gulf killifish, Fundulus grandis: comparing snap-frozen and RNAlater® preserved tissues, Proteomics, 11, 4257, 10.1002/pmic.201100328 Rader, 2008, A unified sample preparation protocol for proteomic and genomic profiling of cervical swabs to identify biomarkers for cervical cancer screening, Proteomics Clin. Appl., 2, 1658, 10.1002/prca.200780146 Saito, 2011, Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection, Front. Microbiol., 2, 10.3389/fmicb.2011.00215 Han, 2013, Label-free quantification for discovering novel biomarkers in the diagnosis and assessment of disease activity in inflammatory bowel disease, J. Dig. Dis., 14, 166, 10.1111/1751-2980.12035 Metz, 2006, Identification of formaldehyde-induced modifications in proteins: reactions with insulin, Bioconjugate Chem., 17, 815, 10.1021/bc050340f Metz, 2003, Identification of formaldehyde-induced modifications in proteins: reactions with model peptides, J. Biol. Chem., 279, 6235, 10.1074/jbc.M310752200 Fox, 1985, Formaldehyde fixation, J. Histochem. Cytochem. Off. J. Histochem. Soc., 33, 845, 10.1177/33.8.3894502 Avaritt, 2014, Decoding the proteome in formalin-fixed paraffin-embedded (FFPE) tissues, J. Proteomics Bioinf., 07 Magdeldin, 2012, Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues, Proteomics, 12, 1045, 10.1002/pmic.201100550 Wakabayashi, 2014, Phosphoproteome analysis of formalin-fixed and paraffin-embedded tissue sections mounted on microscope slides, J. Proteome Res., 13, 915, 10.1021/pr400960r Paulo, 2012, Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry, Pancreas, 41, 175, 10.1097/MPA.0b013e318227a6b7 Ostasiewicz, 2010, Proteome, phosphoproteome, and N-glycoproteome are quantitatively preserved in formalin-fixed paraffin-embedded tissue and analyzable by high-resolution mass spectrometry, J. Proteome Res., 9, 3688, 10.1021/pr100234w Scicchitano, 2009, Protein extraction of formalin-fixed, paraffin-embedded tissue enables robust proteomic profiles by mass spectrometry, J. Histochem. Cytochem., 57, 849, 10.1369/jhc.2009.953497 Addis, 2009, 2-D PAGE and MS analysis of proteins from formalin-fixed, paraffin-embedded tissues, Proteomics, 9, 4329, 10.1002/pmic.200900010 Crockett, 2005, Identification of proteins from formalin-fixed paraffin-embedded cells by LC⿿MS/MS, Lab. Invest., 85, 1405, 10.1038/labinvest.3700343 Wisniewski, 2009, Universal sample preparation method for proteome analysis, Nat. Methods, 6, 359, 10.1038/nmeth.1322 Manza, 2005, Sample preparation and digestion for proteomic analyses using spin filters, Proteomics, 5, 1742, 10.1002/pmic.200401063 Leon, 2013, Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis, Mol. Cell. Proteomics, 12, 2992, 10.1074/mcp.M112.025585 Kawashima, 2014, Efficient extraction of proteins from formalin-fixed paraffin-embedded tissues requires higher concentration of tris(hydroxymethyl) aminomethane, Clin. Proteomics, 11, 4, 10.1186/1559-0275-11-4 Masuda, 2008, Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis, J. Proteome Res., 7, 731, 10.1021/pr700658q Bennike, 2015, Neutrophil extracellular traps in ulcerative colitis: a proteome analysis of intestinal biopsies, Inflammatory Bowel Dis., 10.1097/MIB.0000000000000460 Nielsen, 2008, Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry, Nat. Methods, 5, 459, 10.1038/nmeth0608-459 Dahl, 1981, The reactivity of affinity labels: a kinetic study of the reaction of alkyl halides with thiolate anions⿿a model reaction for protein alkylation, Bioorg. Chem., 10, 329, 10.1016/0045-2068(81)90012-2 G.C. Urbaniak, S. Plous (2013). Research Randomizer (Version 4.0) [Computer software]. Available: http://www.randomizer.org/ (accessed 22.06.13). Vizcaíno, 2014, ProteomeXchange provides globally coordinated proteomics data submission and dissemination, Nat. Biotechnol., 32, 223, 10.1038/nbt.2839 Vizcaíno, 2013, The Proteomics Identifications (PRIDE) database and associated tools: status in 2013, Nucleic Acids Res., 41, D1063, 10.1093/nar/gks1262 Shilov, 2007, The Paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra, Mol. Cell. Proteomics MCP, 6, 1638, 10.1074/mcp.T600050-MCP200 Cox, 2011, A peptide search engine integrated into the MaxQuant environment, J. Proteome Res., 10, 1794, 10.1021/pr101065j Cox, 2008, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat. Biotechnol., 26, 1367, 10.1038/nbt.1511 Bhatia, 2009, Software tool for researching annotations of proteins: open-source protein annotation software with data visualization, Anal. Chem., 81, 9819, 10.1021/ac901335x Deeb, 2012, Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles, Mol. Cell. Proteomics, 11, 77, 10.1074/mcp.M111.015362 Artimo, 2012, ExPASy: SIB bioinformatics resource portal, Nucleic Acids Res., 40, W597, 10.1093/nar/gks400 Rao, 2009, Principal component analysis of proteome dynamics in iron-starved Mycobacterium tuberculosis, J. Proteomics Bioinf., 2, 19, 10.4172/jpb.1000058 Guruprasad, 1990, Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence, Protein Eng., 4, 155, 10.1093/protein/4.2.155 Gasteiger, 2005 Zhang, 2015, Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding, Proteomics, 15, 2568, 10.1002/pmic.201400454 Krokhin, 2006, Deamidation of -Asn-Gly- sequences during sample preparation for proteomics: consequences for MALDI and HPLC-MALDI analysis, Anal. Chem., 78, 6645, 10.1021/ac061017o Dick, 2007, Determination of the origin of the N-terminal pyro-glutamate variation in monoclonal antibodies using model peptides, Biotechnol. Bioeng., 97, 544, 10.1002/bit.21260 Bennike, 2014, A normative study of the synovial fluid proteome from healthy porcine knee joints, J. Proteome Res., 13, 4377, 10.1021/pr500587x Geiger, 2012, Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins, Mol. Cell. Proteomics MCP, 11, 10.1074/mcp.M111.014050 Li, 2005, Anesthesia and post-mortem interval profoundly influence the regulatory serine phosphorylation of glycogen synthase kinase-3 in mouse brain, J. Neurochem., 92, 701, 10.1111/j.1471-4159.2004.02898.x Li, 2002, Post-mortem interval effects on the phosphorylation of signaling proteins, Neuropsychopharmacology, 10.1038/sj.npp.1300112 T.B. Bennike, K. Kastaniegaard, S. Padurariu, M. Gaihede, S. Birkelund, V. Andersen, et al. (2015). Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies (Data in Brief; submitted).