SmartTMT Software

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.

  1. 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.
  2. 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.

Tomahto Screenshot


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.


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.