Use of composite protein database including search result sequences for mass spectrometric analysis of cell secretome

PLoS One. 2015 Mar 30;10(3):e0121692. doi: 10.1371/journal.pone.0121692. eCollection 2015.

Abstract

Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Blood Proteins / genetics
  • Blood Proteins / isolation & purification
  • Cattle
  • Cell Line
  • Culture Media
  • Databases, Protein*
  • HCT116 Cells
  • Humans
  • Proteome / genetics
  • Proteome / isolation & purification
  • Proteomics*
  • Search Engine
  • Species Specificity
  • Tandem Mass Spectrometry

Substances

  • Blood Proteins
  • Culture Media
  • Proteome