• Using Total Ion Current (TIC) Quantitation in Scaffold 3 Software - Comparison to Spectral Counting

  Min Yuan, Susanne Breitkopf, Xuemei Yang (Beth Israel Deaconess Medical Center), Meghana Kulkarni (Harvard Medical School), Xinnong Xiang (Beth Israel Deaconess Medical Center), Jeffrey Engelman (Massachusetts General Hospital), Brian Searle (Proteome SOftware), John M Asara (Beth Israel Deaconess Medical Center & arvard Medical School)
  ASMS 2011

• Probabilistically Assigning Sites of Protein Modification with Scaffold PTM

  Brian C. Searle and Mark Turner (Proteome Software)
  ASMS 2011

• Troubleshooting LTQ and LTQ-Orbitrap LC-MS/MS Systems with MassQC

  Nick Vincent-Maloney, Chris Mason (Proteome Software), and John Klimek (OHSU)
  ABRF 2010

• Improving Sensitivity by Combining Results from Multiple MS/MS

  Brian C. Searle and Mark Turner (Proteome Software)
  ABRF 2007 P17-M

• The Effect of Data Analysis Choices on the Number of Proteins Identified in MS/MS Proteomics Experiments

  Phillip A. Wilmarth (Oregon Health Sciences University), Brian C. Searle (Proteome Software)
  HUPO 2006 W013
  

• Improving Computer Interpretation of Linear Ion Trap Data Using Scaffold

  Brian C. Searle, Mark Turner (Proteome Software)
  HUPO 2006 W006
  

• Flexible, Integrated, and Robust LIMS Information Pipeline withs Results Analytics Views at Scripps Florida

  James P. DeGreef, Denis Bronnikov, Cam Barnard, Brian Searle, Bruce Pascal, Frank Worsley, Mark Turner, Mark Pitman, Sau-Mei Leung, Mike S. Lin
  (Genologics, Proteome Software, Scripps Research Institute - Florida)
  HUPO 2006 W Poster 009
  

• Identifying Peptides the Way Experts Do: A Scientist-Driven Scoring System for Improving MS/MS Peptide Identification Confidence

  Brian C. Searle, Mark Turner (Proteome Software)
  ABRF 2006 #003
  

• Improving Sensitivity by Combining Results from Multiple MS/MS Search Methologies with the Scaffold Computer Algorithm

  Brian C. Searle, James M. Brundege, Mark Turner (Proteome Software)
  HUPO 2005 WP299
  

• Use of Multiple Peptide Identification Programs to Increase Peptide and Protein Identifications in Human Whole Saliva

  Phillip A. Wilmarth, Brian C. Searle, D. Leif Rustvold, Michael A. Riviere, Larry L. David
  (Oregon Health & Science University, Proteome Software)
  ASMS 2005 WP377
  

• Scaffold: A Program to Probabilistically Combine Results from Multiple MS/MS Database Search Engines

  Brian C. Searle, James M. Brundege, Mark Turner (Proteome Software)
  ABRF 2005 P87-T
  

• Quantitation Across Multiple iTRAQ Samples Using Scaffold Q+

  Charles E. Roberts, Jason Nunes, and Brian C. Searle (Proteome Software)
  

• Publishing With Scaffold
  

If you have a poster on protein identification that you'd like posted on this web site, let us know and we will host it.