The lab continues to work with the instrument manufacturer to make our software avilable.
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.
Erickson, B.K., Mintseris, J., Schweppe, D.K., Navarrete-Perea, J., Erickson, A.R., Nusinow, D.P., Paulo, J.A., and Gygi, S.P. (2019). Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows. J Proteome Res 18, 1299-1306.
Schweppe, D.K., Eng, J.K., Bailey, D., Rad, R., Yu, Q., Navarrete-Perea, J., Huttlin, E.L., Erickson, B.K., Paulo, J.A., and Gygi, S.P. (2019). Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics. bioRxiv, 668533.
The Tomahto software provides real-time instrument control and decision making. Tomahto enables simplied implementation of TOMAHAQ targeted assay. It provides an array of functionalities including MS1 peak detection, MS2 real-time peak matching (RTPM), MS2 fragmentation pattern match, SPS ion purity filter, MS3 automatic gain control (AGC), MS3 quant scan insertion, and target peptide close-out. In addition to controlling data acquisition, it also allows real-time data visualization and post-acquisition analysis.
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
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.
AID for TPP
Analysis of Independent Differences (AID) for Thermal Proteome Profiling. AID examines the differences between the fractions of non-denatured protein in order to predict the most likely shifted proteins from thermal proteome profiling experiments.