Field Sample Study Analytical method Statistical method Ref Ecotoxicology and environmental chemistry Mussels   2D-PAGE PCA [81] Plasma samples of Atlantic cods Exposure to alkylphenol SELDI-TOF MS PCA [31] Plasma samples of Atlantic cods Exposure to estrogens SELDI-TOF MS PCA [32] Sydney Rock oysters Exposure to metal contamination 2D-PAGE PCA [2] Digestive gland of the sentinel "blue mussel" Assessment of marine pollution Cell fractionation followed by ion-exchange chromatography and 2-DE Hierarchical clustering  [14] Hake liver and brain extracts Investigation of population variability  2D/DIGE and MS  Hierarchical clustering [15] Clinical biomarker discovery Serum samples   Differential protein biomarker expression and their time-course in coronary syndromes Microarray PCA [83] Serum samples Influence of clotting time on the protein composition Label-free and stable-isotope labeling MS PCA [45] Plasma Identification of biomarkers in patients with acute myocardial infarction 2-D-DiGE PCA [4] Inflamed and non-inflamed colon biopsies Identification of markers for ulcerative colitis 2D-gel electrophoresis and MALDI-TOF MS PCA [5] Serum Protein and peptide profiling in depression MALDI-MS PCA [25]  Serum and pleural effusion Identification of markers for non-small cell lung cancer 2D-DIGE PCA [3] Cell lines Identification of markers for non-small cell lung cancer 2D-DIGE PCA [9] Plasma Effect of a high intake of industrial or ruminant trans fatty acids on healthy men 2DE PCA [8] Brain samples of rats Peptide profiles of exposition to amphetamine MALDI-TOF MS PCA [26] Biopsies Identification of markers for thyroid proliferative diseases SELDI-TOF-MS PCA [34] Plasma   Identification of markers for disease progression for idiopathic pneumonia syndrome following allogeneic stem cell transplantation LC-MS PCA [84] Pancreatic ductal carcinoma cells Effect of Trichostatin A 2D-PAGE PCA [20] Body fluids Development of the analytical method  SOMAmers PCA [85] Plasma Identification of markers in a mouse intestinal tumor model LC-MS/MS Hierarchical clustering [50] Serum Peptidomics in  Crohn's disease Label-free nano-HPLC-MS  Hierarchical clustering [43] Liver Biomarkers for progressive alcoholic steatosis 2-DE  Hierarchical clustering [10] Tissues Different cancers MALDI imaging  Hierarchical clustering [88] Tissues   Characterization of the proteomic changes in Barrett's adenocarcinoma and its premalignant stages MALDI imaging  Hierarchical clustering [89] Assessing measurement reproducibility in biomarker research Reference human serum standard Evaluate the measurement reproducibility SELDI-TOF PCA [33] Serum of cervical cancer patients Development of an improved sample preparation method to perform future comparative analyses of samples from a bank of patients LC-MS  PCA [44]

Table 2: Applications of pattern recognition methods in proteomics.