A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples.

[1]  Andrew D. Palmer,et al.  An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments , 2016, Analytical and Bioanalytical Chemistry.

[2]  R. Casadonte,et al.  Reliable Entity Subtyping in Non-small Cell Lung Cancer by Matrix-assisted Laser Desorption/Ionization Imaging Mass Spectrometry on Formalin-fixed Paraffin-embedded Tissue Specimens* , 2016, Molecular & Cellular Proteomics.

[3]  Michael Becker,et al.  Use of advantageous, volatile matrices enabled by next-generation high-speed matrix-assisted laser desorption/ionization time-of-flight imaging employing a scanning laser beam. , 2015, Rapid communications in mass spectrometry : RCM.

[4]  R. Casadonte,et al.  MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review). , 2015, International journal of oncology.

[5]  A. Walch,et al.  MALDI Imaging mass spectrometry: current frontiers and perspectives in pathology research and practice , 2015, Laboratory Investigation.

[6]  R. Casadonte,et al.  Imaging mass spectrometry to discriminate breast from pancreatic cancer metastasis in formalin‐fixed paraffin‐embedded tissues , 2014, Proteomics.

[7]  Ara Darzi,et al.  Chemo-informatic strategy for imaging mass spectrometry-based hyperspectral profiling of lipid signatures in colorectal cancer , 2014, Proceedings of the National Academy of Sciences.

[8]  Isaiah Norton,et al.  Molecular imaging of drug transit through the blood-brain barrier with MALDI mass spectrometry imaging , 2013, Scientific Reports.

[9]  Theodore Alexandrov,et al.  Imaging mass spectrometry reveals modified forms of histone H4 as new biomarkers of microvascular invasion in hepatocellular carcinomas , 2013, Hepatology.

[10]  N. Ku,et al.  Intermediate filaments of the lung , 2013, Histochemistry and Cell Biology.

[11]  T. Alexandrov MALDI imaging mass spectrometry: statistical data analysis and current computational challenges , 2012, BMC Bioinformatics.

[12]  Marius Ueffing,et al.  MALDI imaging mass spectrometry reveals COX7A2, TAGLN2 and S100-A10 as novel prognostic markers in Barrett's adenocarcinoma. , 2012, Journal of proteomics.

[13]  R. Senetta,et al.  Cancers of unknown primary origin: current perspectives and future therapeutic strategies , 2012, Journal of Translational Medicine.

[14]  M. R. Groseclose,et al.  MALDI imaging mass spectrometry: bridging biology and chemistry in drug development. , 2011, Bioanalysis.

[15]  R. Casadonte,et al.  Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry , 2011, Nature Protocols.

[16]  Liam A. McDonnell,et al.  Multiple Statistical Analysis Techniques Corroborate Intratumor Heterogeneity in Imaging Mass Spectrometry Datasets of Myxofibrosarcoma , 2011, PloS one.

[17]  M. Clyde,et al.  Bayesian nonparametric models for peak identification in maldi-tof mass spectroscopy , 2011, 1107.5407.

[18]  Michel Salzet,et al.  Multivariate analyses for biomarkers hunting and validation through on-tissue bottom-up or in-source decay in MALDI-MSI: application to prostate cancer , 2011, Analytical and bioanalytical chemistry.

[19]  Zoltan Takats,et al.  Mass spectrometry imaging with high resolution in mass and space (HR2 MSI) for reliable investigation of drug compound distributions on the cellular level , 2011, Analytical and bioanalytical chemistry.

[20]  S. Rauser,et al.  Normalization in MALDI-TOF imaging datasets of proteins: practical considerations , 2011, Analytical and bioanalytical chemistry.

[21]  Cheng Bin Liu,et al.  A simple desalting method for direct MALDI mass spectrometry profiling of tissue lipids , 2011, Journal of Lipid Research.

[22]  Johan A. K. Suykens,et al.  Semi-supervised Learning of Sparse Linear Models in Mass Spectral Imaging , 2010, PRIB.

[23]  L. McDonnell,et al.  Peptide and protein imaging mass spectrometry in cancer research. , 2010, Journal of proteomics.

[24]  Peter Hoffmann,et al.  Citric acid antigen retrieval (CAAR) for tryptic peptide imaging directly on archived formalin-fixed paraffin-embedded tissue. , 2010, Journal of proteome research.

[25]  Detlev Suckau,et al.  Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry. , 2010, Journal of proteome research.

[26]  M. Clench,et al.  Novel molecular tumour classification using MALDI–mass spectrometry imaging of tissue micro-array , 2010, Analytical and bioanalytical chemistry.

[27]  Lisa H Cazares,et al.  Imaging Mass Spectrometry of a Specific Fragment of Mitogen-Activated Protein Kinase/Extracellular Signal-Regulated Kinase Kinase Kinase 2 Discriminates Cancer from Uninvolved Prostate Tissue , 2009, Clinical Cancer Research.

[28]  Guy Lapalme,et al.  A systematic analysis of performance measures for classification tasks , 2009, Inf. Process. Manag..

[29]  U. Köthe,et al.  Toward digital staining using imaging mass spectrometry and random forests. , 2009, Journal of proteome research.

[30]  Chao Yang,et al.  Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis , 2009, BMC Bioinformatics.

[31]  Ying Liu,et al.  Matrix factorization techniques for analysis of imaging mass spectrometry data , 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

[32]  Scott T. Rickard,et al.  Comparing Measures of Sparsity , 2008, IEEE Transactions on Information Theory.

[33]  Fred A Hamprecht,et al.  Concise representation of mass spectrometry images by probabilistic latent semantic analysis. , 2008, Analytical chemistry.

[34]  R. Whittal,et al.  Interferences and contaminants encountered in modern mass spectrometry. , 2008, Analytica chimica acta.

[35]  Pierre P Massion,et al.  High‐throughput proteomic analysis of formalin‐fixed paraffin‐embedded tissue microarrays using MALDI imaging mass spectrometry , 2008, Proteomics.

[36]  Michelle L. Reyzer,et al.  MALDI-MS-based imaging of small molecules and proteins in tissues. , 2007, Current opinion in chemical biology.

[37]  R. Liere,et al.  Extended data analysis strategies for high resolution imaging MS: New methods to deal with extremely large image hyperspectral datasets , 2007 .

[38]  Tom Fawcett,et al.  An introduction to ROC analysis , 2006, Pattern Recognit. Lett..

[39]  J. Baatz,et al.  Hemoglobin Is Expressed by Alveolar Epithelial Cells* , 2006, Journal of Biological Chemistry.

[40]  T. Kurihara,et al.  Combined immunohistochemistry of β-catenin, cytokeratin 7, and cytokeratin 20 is useful in discriminating primary lung adenocarcinomas from metastatic colorectal cancer , 2006, BMC Cancer.

[41]  C. Chai,et al.  Role Of TTF‐1, CK20, And CK7 Immunohistochemistry for Diagnosis of Primary and Secondary Lung Adenocarcinoma , 2006, The Kaohsiung journal of medical sciences.

[42]  Jan A Snyman,et al.  Practical Mathematical Optimization: An Introduction to Basic Optimization Theory and Classical and New Gradient-Based Algorithms , 2005 .

[43]  Richard M Caprioli,et al.  Imaging mass spectrometry: a new tool to investigate the spatial organization of peptides and proteins in mammalian tissue sections. , 2002, Current opinion in chemical biology.

[44]  M. Stoeckli,et al.  Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues , 2001, Nature Medicine.

[45]  D. Hunter,et al.  Quantile Regression via an MM Algorithm , 2000 .

[46]  R. Caprioli,et al.  Molecular imaging of biological samples: localization of peptides and proteins using MALDI-TOF MS. , 1997, Analytical chemistry.

[47]  H. B. Mann,et al.  On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other , 1947 .

[48]  Michael Becker,et al.  Tutorial: multivariate statistical treatment of imaging data for clinical biomarker discovery. , 2010, Methods in molecular biology.

[49]  Trevor Hastie,et al.  The Elements of Statistical Learning , 2001 .

[50]  M. Mann,et al.  Analysis of proteins and proteomes by mass spectrometry. , 2001, Annual review of biochemistry.

[51]  H. Sebastian Seung,et al.  Algorithms for Non-negative Matrix Factorization , 2000, NIPS.

[52]  G. Blobel,et al.  Cytokeratins in normal lung and lung carcinomas , 1984, Virchows Archiv. B, Cell pathology including molecular pathology.