Tande
m mass spectro
metry-based shotgun proteo
mics has beco
me a widespread technology for analyzing co
mplex protein
mixtures. A nu
mber of database searching algorith
ms have been developed to assign peptide sequences to tande
m mass spectra. Asse
mbling the peptide identifications to proteins, however, is a challenging issue because
many peptides are shared a
mong
multiple proteins. IDPicker is an open-source protein asse
mbly tool that derives a
mini
mu
m protein list fro
m peptide identifications filtered to a specified False Discovery Rate. Here, we update IDPicker to increase confident peptide identifications by co
mbining
multiple scores produced by database search tools. By segregating peptide identifications for thresholding using both the precursor charge state and the nu
mber of tryptic ter
mini, IDPicker retrieves
more peptides for protein asse
mbly. The new version is
more robust against false positive proteins, especially in searches using
multispecies databases, by requiring additional novel peptides in the parsi
mony process. IDPicker has been designed for incorporation in
many identification workflows by the addition of a graphical user interface and the ability to read identifications fro
m the pepXML for
mat. These advances position IDPicker for high peptide discri
mination and reliable protein asse
mbly in large-scale proteo
mics studies. The source code and binaries for the latest version of IDPicker are available fro
m mc.vanderbilt.edu/" class="extLink">http://fenchurch.mc.vanderbilt.edu/.