Software

RTS-MS3

The lab continues to work with the instrument manufacturer to make the software avilable.  Additional updates will be provided once the publication has been accepted.

The Real-Time Search (RTS-MS3) software provides real-time (<5 ms / spectrum) spectral identification and triggers SPS-MS3 scans that utilize assigned and pure fragment ions for accurate quantitation.   Time consuming SPS-MS3 spectra are only acquired after confident peptide identification, greatly increasing the number of peptides interrogated and reducing the effects of isobaric interference.

Ascore

Search algorithms like Sequest or Mascot often successfully identify the proper peptide sequence, but fail to provide information about the presence or absence of site-determining ions. As a result, users must manually inspect each spectrum to confirm proper site localization. Here, we present a probability-based score, named the Ascore, which measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra

A novel probability-based approach for high-throughput protein phosphorylation analysis and site localization Sean A. Beausoleil, Judit Villen, Scott A. Gerber, John Rush, Steven P Gygi
http://ascore.med.harvard.edu

Motif-X

Motif-x (short for motif extractor) is a software tool designed to extract over-represented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.

Schwartz, D. & Gygi, S.P. (2005). An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nature Biotechnology 23(11), 1391-1398.
http://motif-x.med.harvard.edu/