title: Improving the TFold test for differential shotgun proteomics.
abstract: We present an updated version of the TFold software for pinpointing differentially expressed proteins in shotgun proteomics experiments. Given an FDR bound, the updated approach uses a theoretical FDR estimator to maximize the number of identifications that satisfy both a fold-change cutoff that varies with the t-test P-value as a power law and a stringency criterion that aims to detect lowly abundant proteins. The new version has yielded significant improvements in sensitivity over the previous one.
  
  
  BACKGROUND
  Freely available for academic use at http://pcarvalho.com/patternlab.
authors.affiliation: Carlos Chagas Institute, Fiocruz, Paraná, Brazil. paulo@pcarvalho.com
authors.forename: Paulo C
authors.initials: PC
authors.lastname: Carvalho
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
authors.forename: Valmir C
authors.initials: VC
authors.lastname: Barbosa
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D003627:Data Interpretation, Statistical; D006801:Humans; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins