Addis MF, Tanca A, Pagnozzi D, et al. (2009). Generation of high-quality protein extracts from formalin-fixed, paraffinembedded tissues. Proteomics 9, 3815-3823.
Aggarwal K, Choe LH, and Lee KH. (2006). Shotgun proteomics using the iTRAQ isobaric tags. Briefings Funct Genomics Proteomics 5, 112-120.
Aichler M, Elsner M, Ludyga N, et al. (2013). Clinical response to chemotherapy in oesophageal adenocarcinoma patients is linked to defects in mitochondria. J Pathol 230, 410-419.
Ait-Belkacem R, Berenguer C, Villard C, et al. (2014). MALDI imaging and in-source decay for top-down characterization of glioblastoma. Proteomics 14, 1290-1301.
Ait-Belkacem R, Calligaris D, Sellami L, et al. (2013). Tubulin isoforms identified in the brain by MALDI in-source decay. J Proteomics 79, 172-179.
Alkhas A, Hood BL, Oliver K, et al. (2011). Standardization of a sample preparation and analytical workflow for proteomics of archival endometrial cancer tissue. J Proteome Res 10, 5264-5271.
An HJ, Froehlich JW, and Lebrilla CB.(2009). Determination of glycosylation sites and site-specific heterogeneity in glycoproteins. Curr Opinion Chem Biol 13, 421-426.
Avrameas S, and Uriel J. (1966). [Method of antigen and antibody labelling with enzymes and its immunodiffusion application]. C R Acad Sci Hebd Seances Acad Sci D 262, 2543-2545.
Azimzadeh O, Barjaktarovic Z, Aubele M, et al. (2010). Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics. J Proteome Res 9, 4710-4720.
Baker H, Patel V, Molinolo AA, et al. (2005). Proteome-wide analysis of head and neck squamous cell carcinomas using laser-capture microdissection and tandem mass spectrometry. Oral Oncol 41, 183-199.
Becker KF, Schott C, Hipp S, et al. (2007). Quantitative protein analysis from formalin-fixed tissues: Implications for translational clinical research and nanoscale molecular diagnosis. J Pathol 211, 370-378.
Boersema PJ, Mohammed S, and Heck AJ. (2009). Phosphopeptide fragmentation and analysis by mass spectrometry. J Mass Spectrom 44, 861-878.
Bondarenko PV, Chelius D, and Shaler TA. (2002). Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 74, 4741-4749.
Bonnel D, Longuespee R, Franck J, et al. (2011). Multivariate analyses for biomarkers hunting and validation through ontissue bottom-up or in-source decay in MALDI-MSI: Application to prostate cancer. Anal Bioanal Chem 401, 149-165.
Bonner RF, Emmert-Buck M, Cole K, et al. (1997). Laser capture microdissection: Molecular analysis of tissue. Science 278, 1481-1483.
Boytard L, Spear R, Chinetti-Gbaguidi G, et al. (2013). Role of proinflammatory CD68(+) mannose receptor(-) macrophages in peroxiredoxin-1 expression and in abdominal aortic aneurysms in humans. Arterioscler Thromb Vasc Biol 33, 431-438.
Braakman RB, Luider TM, Martens JW, Foekens JA, and Umar A. (2011). Laser capture microdissection applications in breast cancer proteomics. Methods Mol Biol 755, 143-154.
Braakman RB, Tilanus-Linthorst MM, Liu NQ, et al. (2012). Optimized nLC-MS workflow for laser capture microdissected breast cancer tissue. J Proteomics 75, 2844-2854.
Buckanovich RJ, Sasaroli D, O'Brien-Jenkins A, et al. (2006). Use of immuno-LCM to identify the in situ expression profile of cellular constituents of the tumor microenvironment. Cancer Biol Ther 5, 635-642.
Calligaris D, Longuespee R, Debois D, et al. (2013). Selected protein monitoring in histological sections by targeted MALDI-FTICR in-source decay imaging. Anal Chem 85, 2117-2126.
Calvo E, Camafeita E, Fernandez-Gutierrez B, and Lopez JA. (2011). Applying selected reaction monitoring to targeted proteomics. Expert Rev Proteomics 8, 165-173.
Caprioli RM, Farmer TB, and Gile J. (1997). Molecular imaging of biological samples: Localization of peptides and proteins using MALDI-TOF MS. Anal Chem 69, 4751-4760.
Casadonte R, and Caprioli RM. (2011). Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry. Nat Protoc 6, 1695-1709.
Chen JS, Chen KT, Fan CW, et al. (2010). Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-assisted digestion and iTRAQ labeling mass spectrometry. FEBS J 277, 3028-3038.
Cheng AL, Huang WG, Chen ZC, et al. (2008). Identification of novel nasopharyngeal carcinoma biomarkers by laser capture microdissection and proteomic analysis. Clin Cancer Res 14, 435-445.
Christin C, Bischoff R, and Horvatovich P. (2011). Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC-MS for biomarker discovery. Talanta 83, 1209-1224.
Chu WS, Liang Q, Liu J, et al. (2005). A nondestructive molecule extraction method allowing morphological and molecular analyses using a single tissue section. Lab Invest 85, 1416-1428.
Coons AH, and Kaplan MH. (1950). Localization of antigen in tissue cells; Improvements in a method for the detection of antigen by means of fluorescent antibody. J Exp Med 91, 1-13.
Cox J, and Mann M. (2009). Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap. J Am Soc Mass Spectrom 20, 1477-1485.
Craven RA, Cairns DA, Zougman A, Harnden P, Selby PJ, and Banks RE. (2013). Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: Assessment of overall technical variability and the impact of block age. Proteomics Clin Appl 7, 273-282.
Crockett DK, Lin Z, Vaughn CP, Lim MS, and Elenitoba-Johnson KS. (2005). Identification of proteins from formalinfixed paraffin-embedded cells by LC-MS/MS. Lab Invest 85, 1405-1415.
Desiere F, Deutsch EW, King NL, et al., (2006). The PeptideAtlas project. Nucleic Acids Res 34, D655-658.
Desouza L, Diehl G, Rodrigues MJ, et al. (2005). Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and cICAT with multidimensional liquid chromatography and tandem mass spectrometry. J Proteome Res 4, 377-386.
Deterding LJ, Moseley MA, Tomer KB, and Jorgenson JW. (1991). Nanoscale separations combined with tandem mass spectrometry. J Chromatog 554, 73-82.
Diament BJ, and Noble WS. (2011). Faster SEQUEST searching for peptide identification from tandem mass spectra. J Proteome Res 10, 3871-3879.
El Ayed M, Bonnel D, Longuespee R, et al. (2010). MALDI imaging mass spectrometry in ovarian cancer for tracking, identifying, and validating biomarkers. Med Sci Monit 16, BR233-245.
Emmert-Buck MR, Bonner RF, Smith PD, et al. (1996). Laser capture microdissection. Science 274, 998-1001.
Espina V, Milia J, Wu G, Cowherd S, and Liotta LA. (2006a). Laser capture microdissection. Methods Mol Biol 319, 213-229.
Fend F, Kremer M, and Quintanilla-Martinez L. (2000). Laser capture microdissection: Methodical aspects and applications with emphasis on immuno-laser capture microdissection. Pathobiology 68, 209-214.
Fenn JB, Mann M, Meng CK, Wong SF, and Whitehouse CM. (1989). Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71.
Fey SJ, and Larsen PM. (2001). 2D or not 2D. Two-dimensional gel electrophoresis. Curr Opinion Chem Biol 5, 26-33.
Ficarro SB, McCleland ML, Stukenberg PT, et al. (2002). Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nature Biotechnol 20, 301-305.
Fowler CB, Waybright TJ, Veenstra TD, O'leary TJ, and Mason JT. (2012). Pressure-assisted protein extraction: A novel method for recovering proteins from archival tissue for proteomic analysis. J Proteome Res 11, 2602-2608.
Fraenkel-Conrat H, and Olcott HS. (1946). Reaction of formaldehyde with proteins; Participation of the guanidyl groups and evidence of crosslinking. J Am Chem Soc 68, 34-37.
Fraenkel-Conrat H, and Olcott HS. (1948a). The reaction of formaldehyde with proteins; Cross-linking between amino and primary amide or guanidyl groups. J Am Chem Soc 70, 2673-2684.
Fraenkel-Conrat H, and Olcott HS. (1948b). Reaction of formaldehyde with proteins; Cross-linking of amino groups with phenol, imidazole, or indole groups. J Biol Chem 174, 827-843.
Franck J, Longuespee R, Wisztorski M, et al. (2010). MALDI mass spectrometry imaging of proteins exceeding 30,000 daltons. Med Sci Monit 16, BR293-299.
Frank A, and Pevzner P. (2005). PepNovo: De novo peptide sequencing via probabilistic network modeling. Anal Chem 77, 964-973.
Garbis SD, Tyritzis SI, Roumeliotis T, et al. (2008). Search for potential markers for prostate cancer diagnosis, prognosis and treatment in clinical tissue specimens using amine-specific isobaric tagging (iTRAQ) with two-dimensional liquid chromatography and tandem mass spectrometry. J Proteome Res 7, 3146-3158.
Garden RW, Moroz LL, Moroz TP, Shippy SA, and Sweedler JV. (1996). Excess salt removal with matrix rinsing: Direct peptide profiling of neurons from marine invertebrates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Mass Spectrom 31, 1126-1130.
Giusti L, and Lucacchini A. (2013). Proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 10, 165-177.
Gu Y, Wu SL, Meyer JL, et al. (2007). Proteomic analysis of high-grade dysplastic cervical cells obtained from ThinPrep slides using laser capture microdissection and mass spectrometry. J Proteome Res 6, 4256-4268.
Guo T, Wang W, Rudnick PA, et al. (2007). Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem 55, 763-772.
Gustafsson JO, Oehler MK, McColl SR, and Hoffmann P. (2010). Citric acid antigen retrieval (CAAR) for tryptic peptide imaging directly on archived formalin-fixed paraffinembedded tissue. J Proteome Res 9, 4315-4328.
Hardman M, and Makarov AA. (2003). Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal Chem 75, 1699-1705.
Harris GA, Nicklay JJ, and Caprioli RM. (2013). Localized in situ hydrogel-mediated protein digestion and extraction technique for on-tissue analysis. Anal Chem 85, 2717-2723.
Hatakeyama H, Kondo T, Fujii K, et al. (2006). Protein clusters associated with carcinogenesis, histological differentiation and nodal metastasis in esophageal cancer. Proteomics 6, 6300-6316.
Higgs RE, Knierman MD, Gelfanova V, Butler JP, and Hale JE. (2005). Comprehensive label-free method for the relative quantification of proteins from biological samples. J Proteome Res 4, 1442-1450.
Hill JJ, Tremblay TL, Pen A, et al. (2011). Identification of vascular breast tumor markers by laser capture microdissection and label-free LC-MS. J Proteome Res 10, 2479-2493.
Hillenkamp F, and Karas M. (1990). Mass spectrometry of peptides and proteins by matrix-assisted ultraviolet laser desorption/ionization. Methods Enzymol 193, 280-295.
Hirosawa M, Hoshida M, Ishikawa M, and Toya T. (1993). MASCOT: Multiple alignment system for protein sequences based on three-way dynamic programming. Computer Applic Biosci CABIOS 9, 161-167.
Hosako M, Muto T, Nakamura Y, et al. (2012). Proteomic study of malignant pleural mesothelioma by laser microdissection and two-dimensional difference gel electrophoresis identified cathepsin D as a novel candidate for a differential diagnosis biomarker. J Proteomics 75, 833-844.
Hwang SI, Thumar J, Lundgren DH, et al. (2007). Direct cancer tissue proteomics: A method to identify candidate cancer biomarkers from formalin-fixed paraffin-embedded archival tissues. Oncogene 26, 65-76.
Ikeda K, Monden T, Kanoh T, et al. (1998). Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin-embedded tissue sections. J Histochem Cytochem 46, 397-403.
Jackson SN, Ugarov M, Egan T, et al. (2007). MALDI-ion mobility-TOFMS imaging of lipids in rat brain tissue. J Mass Spectrom 42, 1093-1098.
Jadoul L, Malherbe C, Calligaris D, et al. (2014). Matrixassisted laser desorption/ionization mass spectrometry and Raman spectroscopy: An interesting complementary approach for lipid detection in biological tissues. Eur J Lipid Sci Technol 116, In press.
Jiang X, Feng S, Tian R, Ye M, and Zou H. (2007). Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues. J Proteome Res 6, 1038-1047.
Jimenez CR, Van Veelen PA, Li KW, et al. (1994). Neuropeptide expression and processing as revealed by direct matrix-assisted laser desorption ionization mass spectrometry of single neurons. J Neurochem 62, 404-407.
Johann DJ, Rodriguez-Canales J, Mukherjee S, et al. (2009). Approaching solid tumor heterogeneity on a cellular basis by tissue proteomics using laser capture microdissection and biological mass spectrometry. J Proteome Res 8, 2310-2318.
Jones EA, Deininger SO, Hogendoorn PC, Deelder AM, and Mcdonnell LA. (2012). Imaging mass spectrometry statistical analysis. J Proteomics 75, 4962-4989.
Jones P, Cote RG, Martens L, et al. (2006). PRIDE: A public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res 34, D659-663.
Kakimoto Y, Tsuruyama T, Yamamoto T, et al. (2012). Novel in situ pretreatment method for significantly enhancing the signal in MALDI-TOF MS of formalin-fixed paraffin-embedded tissue sections. PLoS One 7, e41607.
Kelly RT, Tolmachev AV, Page JS, Tang K, and Smith RD. (2010). The ion funnel: Theory, implementations, and applications. Mass Spectrom Rev 29, 294-312.
Kim T, Tolmachev AV, Harkewicz R, et al. (2000). Design and implementation of a new electrodynamic ion funnel. Anal Chem 72, 2247-2255.
Kiyonami R, Schoen A, Prakash A, et al. (2011). Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol Cell Proteomics 10, M110002931.
Kocher T, Pichler P, Mazanek M, Swart R, and Mechtler K. (2011). Altered Mascot search results by changing the m/z range of MS/MS spectra: Analysis and potential applications. Anal Bioanal Chem 400, 2339-2347.
Kolble K. (2000). The LEICA microdissection system: Design and applications. J Mol Med (Berl) 78, B24-25.
Kurman RJ, and Shih Ie M. (2010). The origin and pathogenesis of epithelial ovarian cancer: A proposed unifying theory. Am J Surg Pathol 34, 433-443.
Lam H, Deutsch EW, Eddes JS, et al., (2007). Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7, 655-667.
Leong AS, Milios J, and Duncis CG. (1988). Antigen preservation in microwave-irradiated tissues: A comparison with formaldehyde fixation. J Pathol 156, 275-282.
Leong AS, and Wright J. (1987). The contribution of immunohistochemical staining in tumour diagnosis. Histopathology 11, 1295-1305.
Li B, An HJ, Hedrick JL, and Lebrilla CB. (2009). Collisioninduced dissociation tandem mass spectrometry for structural elucidation of glycans. Methods Mol Biol 534, 133-145.
Li C, Hong Y, Tan YX, et al. (2004). Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol Cell Proteomics 3, 399-409.
Li C, Yi H, Tan YX, et al. (2008). Analysis of microdissected cells by two-dimensional LC-MS approaches. Methods Mol Biol 428, 193-208.
Lilley KS, and Friedman DB. (2004). All about DIGE: Quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics 1, 401-409.
Liu NQ, Braakman RB, Stingl C, et al. (2012). Proteomics pipeline for biomarker discovery of laser capture microdissected breast cancer tissue. J Mammary Gland Biol Neoplasia 17, 155-164.
Liu Y, Wu J, Yan G, et al. (2010). Proteomic analysis of prolactinoma cells by immuno-laser capture microdissection combined with online two-dimensional nano-scale liquid chromatography/mass spectrometry. Proteome Sci 8, 2.
Longuespee R, Boyon C, Castellier C, et al. (2012). The Cterminal fragment of the immunoproteasome PA28S (Reg alpha) as an early diagnosis and tumor-relapse biomarker: Evidence from mass spectrometry profiling. Histochem Cell Biol 138, 141-154.
Longuespee R, Boyon C, Desmons A, et al. (2014a). Spectroimmunohistochemistry: A novel form of MALDI mass spectrometry imaging coupled to immunohistochemistry for tracking antibodies. Omics 18, 132-141.
Longuespee R, Gagnon H, Boyon C, et al. (2013). Proteomic analyses of serous and endometrioid epithelial ovarian cancers. Cases studies: Molecular insights of a possible histological etiology of serous ovarian cancer. Proteomics Clin Appl 7, 337-354.
Longuespee R, Tastet C, Desmons A, et al. (2014b). HFIP extraction followed by 2D CTAB-SDS PAGE separation: A new methodology for protein identification from tissue sections after MALDI mass spectrometry profiling for personalized medicine research. OMICS 18, 374-384.
Maes E, Broeckx V, Mertens I, et al. (2013). Analysis of the formalin-fixed paraffin-embedded tissue proteome: Pitfalls, challenges, and future prospectives. Amino Acids 45, 205-218.
Magdeldin S, and Yamamoto T. (2012). Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Proteomics 12, 1045-1058.
Maier SK, Hahne H, Moghaddas Gholami A, et al. (2013). Comprehensive identification of proteins from MALDI imaging. Mol Cell Proteomics 10, 2901-2910.
Makarov A, Denisov E, Kholomeev A, et al. (2006). Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer. Anal Chem 78, 2113-2120.
Makarov A, Denisov E, and Lange O. (2009). Performance evaluation of a high-field Orbitrap mass analyzer. J Am Soc Mass Spectrom 20, 1391-1396.
Mann M, and Kelleher NL. (2008). Precision proteomics: The case for high resolution and high mass accuracy. Proc Natl Acad Sci USA 105, 18132-18138.
Mann M, and Wilm M. (1994). Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal Chem 66, 4390-4399.
Marginean I, Page JS, Tolmachev AV, Tang K, and Smith RD. (2010). Achieving 50% ionization efficiency in subambient pressure ionization with nanoelectrospray. Anal Chem 82, 9344-9349.
Mason DY, and Sammons R. (1978). Alkaline phosphatase and peroxidase for double immunoenzymatic labelling of cellular constituents. J Clin Pathol 31, 454-460.
Masselon C, Anderson GA, Harkewicz R, Bruce JE, Pasa-Tolic L, and Smith RD. (2000). Accurate mass multiplexed tandem mass spectrometry for high-throughput polypeptide identification from mixtures. Anal Chem 72, 1918-1924.
May C, Brosseron F, Chartowski P, Meyer HE, and Marcus K. (2012). Differential proteome analysis using 2D-DIGE. Methods Mol Biol 893, 75-82.
McDonnell LA, Corthals GL, Willems SM, Van Remoortere A, Van Zeijl RJ, and Deelder AM. (2010). Peptide and protein imaging mass spectrometry in cancer research. J Proteomics 73, 1921-1944.
Meding S, Balluff B, Elsner M, et al., (2012). Tissue-based proteomics revealsFXYD3, S100A11 andGSTM3as novel markers for regional lymph nodemetastasis in colon cancer. J Pathol 228, 459-470.
Meding S, Martin K, Gustafsson OJ, et al. (2013). Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues. J Proteome Res 12, 308-315.
Michalski A, Damoc E, Hauschild JP, et al. (2011). Mass spectrometry-based proteomics using Q Exactive, a highperformance benchtop quadrupole Orbitrap mass spectrometer. Mol Cell Proteomics 10, M111011015.
Micke P, Ostman A, Lundeberg J, and Ponten F. (2005). Laserassisted cell microdissection using the PALM system. Methods Mol Biol 293, 151-166.
Muraoka S, Kume H, Watanabe S, et al. (2012). Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples. J Proteome Res 11, 4201-4210.
Nadji M. (1986). Immunoperoxidase techniques. I. Facts and artifacts. Am J Dermatopathol 8, 32-36.
Nagaraj N, D'souza RC, Cox J, Olsen JV, and Mann M. (2010). Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res 9, 6786-6794.
Nakamura N, Ruebel K, Jin L, Qian X, Zhang H, and Lloyd RV. (2007). Laser capture microdissection for analysis of single cells. Methods Mol Med 132, 11-18.
Nakane PK. (1968). Simultaneous localization of multiple tissue antigens using the peroxidase-labeled antibody method: A study on pituitary glands of the rat. J Histochem Cytochem 16, 557-560.
Nakane PK, and Pierce GB, Jr. (1966). Enzyme-labeled antibodies: Preparation and application for the localization of antigens. J Histochem Cytochem 14, 929-931.
Nakatani S, Wei M, Ishimura E, et al. (2012). Proteome analysis of laser microdissected glomeruli from formalin-fixed paraffin-embedded kidneys of autopsies of diabetic patients: Nephronectin is associated with the development of diabetic glomerulosclerosis. Nephrol Dial Transplant 27, 1889-1897.
Narumi R, Murakami T, Kuga T, et al. (2012). A strategy for large-scale phosphoproteomics and SRM-based validation of human breast cancer tissue samples. J Proteome Res 11, 5311-5322.
Nazarian J, Santi M, Hathout Y, and Macdonald TJ. (2008). Protein profiling of formalin fixed paraffin embedded tissue: Identification of potential biomarkers for pediatric brainstem glioma. Proteomics Clin Appl 2, 915-924.
Neilson KA, Ali NA, Muralidharan S, et al.,(2011). Less label, more free: Approaches in label-free quantitative mass spectrometry. Proteomics 11, 535-553.
Nirmalan NJ, Harnden P, Selby PJ, and Banks RE. (2008). Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. Mol Biosyst 4, 712-720.
Nirmalan NJ, Harnden P, Selby PJ, and Banks RE. (2009). Development and validation of a novel protein extraction methodology for quantitation of protein expression in formalin-fixed paraffin-embedded tissues using western blotting. J Pathol 217, 497-506.
Nirmalan NJ, Hughes C, Peng J, et al. (2011). Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations. J Proteome Res 10, 896-906.
Nishimura T, Nomura M, Tojo H, et al. (2010). Proteomic analysis of laser-microdissected paraffin-embedded tissues: (2) MRM assay for stage-related proteins upon nonmetastatic lung adenocarcinoma. J Proteomics 73, 1100-1110.
Oda Y, Nagasu T, and Chait BT. (2001). Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome. Nature Biotechnol 19, 379-382.
Olsen JV, Schwartz JC, Griep-Raming J, et al, (2009). A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics 8, 2759-2769.
Ostasiewicz P, Zielinska DF, Mann M, and Wisniewski JR. (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, 3688-3700.
Page JS, Tang K, Kelly RT, and Smith RD. (2008). Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry. Anal Chem 80, 1800-1805.
Page JS, Tolmachev AV, Tang K, and Smith RD. (2006). Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel. J Am Soc Mass Spectrom 17, 586-592.
Palmer-Toy DE, Krastins B, Sarracino DA, Nadol JB, Jr., and Merchant SN. (2005). Efficient method for the proteomic analysis of fixed and embedded tissues. J Proteome Res 4, 2404-2411.
Palmer-Toy DE, Sarracino DA, Sgroi D, Levangie R, and Leopold PE. (2000). Direct acquisition of matrix-assisted laser desorption/ionization time-of-flight mass spectra from laser capture microdissected tissues. Clin Chem 46, 1513-1516.
Pan S, Chen R, Stevens T, et al. (2011). Proteomics portrait of archival lesions of chronic pancreatitis. PLoS One 6, e27574.
Panchaud A, Jung S, Shaffer SA, Aitchison JD, and Goodlett DR. (2011). Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem 83, 2250-2257.
Panchaud A, Scherl A, Shaffer SA, et al. (2009). Precursor acquisition independent from ion count: How to dive deeper into the proteomics ocean. Anal Chem 81, 6481-6488.
Pietersen CY, Lim MP, and Woo TU. (2009). Obtaining high quality RNA from single cell populations in human postmortem brain tissue. J Vis Exp 30, 1444.
Prieto DA, Hood BL, Darfler MM, et al. (2005). Liquid Tissue: Proteomic profiling of formalin-fixed tissues. Biotechniques Suppl, 38, 32-35.
Rezaul K, Thumar JK, Lundgren DH, et al. (2010). Differential protein expression profiles in estrogen receptor-positive and-negative breast cancer tissues using label-free quantitative proteomics. Genes Cancer 1, 251-271.
Rompp A, and Spengler B. (2013). Mass spectrometry imaging with high resolution in mass and space. Histochem Cell Biol 139, 759-783.
Sanders ME, Dias EC, Xu BJ, et al. (2008). Differentiating proteomic biomarkers in breast cancer by laser capture microdissection and MALDI MS. J Proteome Res 7, 1500-1507.
Shaffer SA, Prior DC, Anderson GA, Udseth HR, and Smith RD. (1998). An ion funnel interface for improved ion focusing and sensitivity using electrospray ionization mass spectrometry. Anal Chem 70, 4111-4119.
Shekouh AR, Thompson CC, Prime W, et al, (2003). Application of laser capture microdissection combined with twodimensional electrophoresis for the discovery of differentially regulated proteins in pancreatic ductal adenocarcinoma. Proteomics 3, 1988-2001.
Shi H, Hood KA, Hayes MT, and Stubbs RS. (2011). Proteomic analysis of advanced colorectal cancer by laser capture microdissection and two-dimensional difference gel electrophoresis. J Proteomics 75, 339-351.
Shi SR, Liu C, Balgley BM, Lee C, and Taylor CR. (2006). Protein extraction from formalin-fixed, paraffin-embedded tissue sections: Quality evaluation by mass spectrometry. J Histochem Cytochem 54, 739-743.
Shvartsburg AA, Seim TA, Danielson WF, et al. (2013). Highdefinition differential ion mobility spectrometry with resolving power up to 500. J Am Soc Mass Spectrom 24, 109-114.
Shvartsburg AA, Singer D, Smith RD, and Hoffmann R. (2011). Ion mobility separation of isomeric phosphopeptides from a protein with variant modification of adjacent residues. Anal Chem 83, 5078-5085.
Singer SJ. (1959). Preparation of an electron-dense antibody conjugate. Nature 183, 1523-1524.
Skvortsov S, Schafer G, Stasyk T, et al. (2011). Proteomics profiling of microdissected low-and high-grade prostate tumors identifies Lamin A as a discriminatory biomarker. J Proteome Res 10, 259-268.
Stahl B, Linos A, Karas M, Hillenkamp F, and Steup M. (1997). Analysis of fructans from higher plants by matrix-assisted laser desorption/ionization mass spectrometry. Anal Biochem 246, 195-204.
Stauber J, Ayed ME, Wisztorski M, Salzet M, and Fournier I. (2010). Specific MALDI-MSI: Tag-Mass. Methods Mol Biol 656, 339-361.
Sternberger LA, Hardy PH, Jr., Cuculis JJ, and Meyer HG. (1970). The unlabeled antibody enzyme method of immu-nohistochemistry: Preparation and properties of soluble antigen-antibody complex (horseradish peroxidase- antihorseradish peroxidase) and its use in identification of spirochetes. J Histochem Cytochem 18, 315-333.
Stingl C, Van Vilsteren FG, Guzel C, et al. (2011). Reproducibility of protein identification of selected cell types in Barrett's esophagus analyzed by combining laser-capture microdissection and mass spectrometry. J Proteome Res 10, 288-298.
Sugihara Y, Taniguchi H, Kushima R, et al. (2013). Laser microdissection and two-dimensional difference gel electrophoresis reveal proteomic intra-tumor heterogeneity in colorectal cancer. J Proteomics 78, 134-147.
Swanson PE. (1997). HIERanarchy: The state of the art in immunohistochemistry. Am J Clin Pathol 107, 139-140.
Tabb DL, Fernando CG, and Chambers MC. (2007). MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res 6, 654-661.
Tabb DL, Ma ZQ, Martin DB, Ham AJ, and Chambers MC. (2008). DirecTag: Accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res 7, 3838-3846.
Tabb DL, Saraf A, and Yates JR, 3rd. (2003). GutenTag: Highthroughput sequence tagging via an empirically derived fragmentation model. Anal Chem 75, 6415-6421.
Tanaka K, Waki H, Ido Y, et al. (1988). Protein and polymer analyses up to m/z 100 000 by laser ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 2, 151-153.
Tang K, Page JS, Marginean I, Kelly RT, and Smith RD. (2011). Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface. J Am Soc Mass Spectrom 22, 1318-1325.
Tangrea MA, Mukherjee S, Gao B, et al. (2011). Effect of immunohistochemistry on molecular analysis of tissue samples: Implications for microdissection technologies. J Histochem Cytochem 59, 591-600.
Thakur D, Rejtar T, Wang D, et al. (2011). Microproteomic analysis of 10,000 laser captured microdissected breast tumor cells using short-range sodium dodecyl sulfate-polyacrylamide gel electrophoresis and porous layer open tubular liquid chromatography tandem mass spectrometry. J Chromatogr A 1218, 8168-8174.
Tian Y, Gurley K, Meany DL, Kemp CJ, and Zhang H. (2009). N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues. J Proteome Res 8, 1657-1662.
Umar A, Kang H, Timmermans AM, Look MP, et al. (2009). Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer. Mol Cell Proteomics 8, 1278-1294.
Umar A, Luider TM, Foekens JA, and Pasa-Tolic L. (2007). NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells. Proteomics 7, 323-329.
Van Remoortere A, Van Zeijl RJ, Van Den Oever N, et al. (2010). MALDI imaging and profiling MS of higher mass proteins from tissue. J Am Soc Mass Spectrom 21, 1922-1929.
Van Strien FJ, Jespersen S, Van Der Greef J, Jenks BG, and Roubos EW. (1996). Identification of POMC processing products in single melanotrope cells by matrix-assisted laser desorption/ionization mass spectrometry. FEBS Lett 379, 165-170.
Venable JD, Dong MQ, Wohlschlegel J, Dillin A, and Yates JR. (2004). Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nature Meth 1, 39-45.
Vizcaino JA, Cote R, Reisinger F, et al. (2009). A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9, 4276-4283.
Vogt A, Fuerholzner B, Kinkl N, Boldt K, and Ueffing M. (2013). Isotope coded protein labeling coupled immunoprecipitation (ICPL-IP): A novel approach for quantitative protein complex analysis from native tissue. Mol Cell Proteomics 12, 1395-1406.
Wang G, Wu WW, Zeng W, Chou CL, and Shen RF. (2006). Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes. J Proteome Res 5, 1214-1223.
Wang LN, Tong SW, Hu HD, et al. (2012). Quantitative proteome analysis of ovarian cancer tissues using a iTRAQ approach. J Cell Biochem 113, 3762-3772.
Wells JM, and Mcluckey SA. (2005). Collision-induced dissociation (CID) of peptides and proteins. Methods Enzymol 402, 148-185.
Wiesner J, Premsler T, and Sickmann A. (2008). Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications. Proteomics 8, 4466-4483.
Willems SM, Van Remoortere A, Van Zeijl R, Deelder AM, Mcdonnell LA, and Hogendoorn PC. (2010). Imaging mass spectrometry of myxoid sarcomas identifies proteins and lipids specific to tumour type and grade, and reveals biochemical intratumour heterogeneity. J Pathol 222, 400-409.
Wisniewski JR, Dus K, and Mann M. (2013). Proteomic workflow for analysis of archival formalin-fixed and paraffinembedded clinical samples to a depth of 10 000 proteins. Proteomics Clin Appl 7, 225-233.
Wisniewski JR, Ostasiewicz P, and Mann M. (2011). High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J Proteome Res 10, 3040-3049.
Wisztorski M, Fatou B, Franck J, et al. (2013). Microproteomics by liquid extraction surface analysis: Application to FFPE tissue to study the fimbria region of tubo-ovarian cancer. Proteomics Clin Appl 7, 234-240.
Wong KF, and Luk JM. (2012). Discovery of lamin B1 and vimentin as circulating biomarkers for early hepatocellular carcinoma. Methods Mol Biol 909, 295-310.
Xu BJ, Caprioli RM, Sanders ME, and Jensen RA. (2002). Direct analysis of laser capture microdissected cells by MALDI mass spectrometry. J Am Soc Mass Spectrom 13, 1292-1297.
Xu BJ, Li J, Beauchamp RD, et al. (2009). Identification of early intestinal neoplasia protein biomarkers using laser capture microdissection and MALDI MS. Mol Cell Proteomics 8, 936-945.
Xu BJ, Shyr Y, Liang X, et al. (2005). Proteomic patterns and prediction of glomerulosclerosis and its mechanisms. J Am Soc Nephrol 16, 2967-2975.
Xu H, Yang L, Wang W, et al. (2008). Antigen retrieval for proteomic characterization of formalin-fixed and paraffinembedded tissues. J Proteome Res 7, 1098-1108.
Yao H, Zhang Z, Xiao Z, et al. (2009). Identification of metastasis associated proteins in human lung squamous carcinoma using two-dimensional difference gel electrophoresis and laser capture microdissection. Lung Cancer 65, 41-48.
Yates JR, 3rd, Morgan SF, Gatlin CL, Griffin PR, and Eng JK. (1998). Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractive analysis. Anal Chem 70, 3557-3565.
Zang L, Palmer Toy D, Hancock WS, Sgroi DC, and Karger BL. (2004). Proteomic analysis of ductal carcinoma of the breast using laser capture microdissection, LC-MS, and 16O/18O isotopic labeling. J Proteome Res 3, 604-612.
Zanni KL, and Chan GK. (2011). Laser capture microdissection: Understanding the techniques and implications for molecular biology in nursing research through analysis of breast cancer tumor samples. Biol Res Nurs 13, 297-305.
Zhang D, Tai LK, Wong LL, Chiu LL, Sethi SK, and Koay ES. (2005). Proteomic study reveals that proteins involved in metabolic and detoxification pathways are highly expressed in HER-2/neu-positive breast cancer. Mol Cell Proteomics 4, 1686-1696.
Zhang H, Li XJ, Martin DB, and Aebersold R. (2003). Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nature Biotechnol 21, 660-666.
Zhang J, Xin L, Shan B, et al. (2012). PEAKS DB: De novo sequencing assisted database search for sensitive and accurate peptide identification. Mol Cell Proteomics 11, M111010587.
Zhang Y, Tang H, Cai J, et al. (2011). Ovarian cancer-associated fibroblasts contribute to epithelial ovarian carcinoma metastasis by promoting angiogenesis, lymphangiogenesis and tumor cell invasion. Cancer Lett 303, 47-55.
Zhou G, Li H, Decamp D, et al. (2002). 2D differential in-gel electrophoresis for the identification of esophageal scans cell cancer-specific protein markers. Mol Cell Proteomics 1, 117-124.
Zhou H, Watts JD, and Aebersold R. (2001). A systematic approach to the analysis of protein phosphorylation. Nature Biotechnol 19, 375-378.
Zhu J, Nie S, Wu J, and Lubman DM. (2013). Target proteomic profiling of frozen pancreatic CD24 + adenocarcinoma tissues by immuno-laser capture microdissection and nano-LCMS/MS. J Proteome Res 12, 2791-2804.