title: Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.
abstract: Electron transfer dissociation (ETD) is an alternative fragmentation technique to CID that has recently become commercially available. ETD has several advantages over CID. It is less prone to fragmenting amino acid side chains, especially those that are modified, thus yielding fragment ion spectra with more uniform peak intensities. Further, precursor ions of longer peptides and higher charge states can be fragmented and identified. However, analysis of ETD spectra has a few important differences that require the optimization of the software packages used for the analysis of CID data or the development of specialized tools. We have adapted the Trans-Proteomic Pipeline to process ETD data. Specifically, we have added support for fragment ion spectra from high-charge precursors, compatibility with charge-state estimation algorithms, provisions for the use of the Lys-C protease, capabilities for ETD spectrum library building, and updates to the data formats to differentiate CID and ETD spectra. We show the results of processing data sets from several different types of ETD instruments and demonstrate that application of the ETD-enhanced Trans-Proteomic Pipeline can increase the number of spectrum identifications at a fixed false discovery rate by as much as 100% over native output from a single sequence search engine.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA. edeutsch@systemsbiology.org
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: David
authors.initials: D
authors.lastname: Shteynberg
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.forename: Christine
authors.initials: C
authors.lastname: Carapito
authors.forename: Priska D
authors.initials: PD
authors.lastname: von Haller
authors.forename: Natalie
authors.initials: N
authors.lastname: Tasman
authors.forename: Luis
authors.initials: L
authors.lastname: Mendoza
authors.forename: Terry
authors.initials: T
authors.lastname: Farrah
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D019295:Computational Biology / Q000379:methods*; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides