By default, the Proteome Discoverer application supports the following search engines:

  • Sequest HT
  • MSPepSearch
  • Mascot

  • NOTE

    You must access a Mascot server to use the Mascot node for Proteome Discoverer. The Workflow Editor includes these nodes.

  • CHIMERYS™

NOTE

You must have a permanent Proteome Discoverer license and a CHIMERYS account to use the CHIMERYS node for Proteome Discoverer.

  • Comet

You can find additional search engine nodes in the third-party node installer, or you can download search engine nodes from third-party developer sites.

The following table describes the Proteome Discoverer search engines.

Search engines

Search engine

Description

Sequest HT

The Sequest HT search engine is distributed by Thermo Fisher Scientific. It can analyze the following data types:

  • Electron-transfer dissociation (ETD)
  • Electron transfer dissociation with HCD activation (EThcD)
  • Electron-capture dissociation (ECD)
  • Collision-induced dissociation (CID)
  • High-energy collision-induced dissociation (HCD)
  • Pulsed Q collision-induced dissociation (PQD)
  • Ultraviolet photodissociation (UVPD)

ETD and ECD generate primarily c and z fragment ions with preferences for precursor ion charge states of +3 or higher. CID and HCD generate primarily b and y fragment ions with preferences for precursor ion charge states of +3 or lower. PQD and HCD do not exhibit a low-mass cutoff and are good for reporter-ion experiments.

Frequently, peptides identified by CID, PQD, or HCD are not observed with ETD or ECD, and vice versa. This way, combining results from, for example, CID and ETD can enhance sequence coverage. Frequently, CID and ETD identify the same peptides, often with different precursor ion charge states. Therefore, combining ETD and CID results improves confidence in identifications.

The Sequest HT search engine calculates XCorr scores for peptide matches and provides the peptide matches that have the best XCorr score for each spectrum.

Mascot

The Mascot search engine, created by Matrix Science, uses mass spectrometry data to identify proteins from primary sequence databases. For more details on Mascot, visit https://www.matrixscience.com/.

CHIMERYS

A scalable, cloud-based service that predicts accurate peptide properties using the deep learning-based INFERYS framework. Using intensity-based deconvolution of chimeric peptide MS2 spectra, CHIMERYS unlocks unprecedented analysis depth for proteomics data analysis.

CHIMERYS supports the analysis of data-dependent MS/MS spectra with the following properties:

  • HCD and CID fragmentation
  • Orbitrap and Ion Trap mass spectrometry detection
  • Label-free, TMT and TMTpro quantification
  • Phosphorylation identification

After data is uploaded to the cloud service, the intelligent search algorithm CHIMERYS performs a coarse first search for recalibration. Subsequently, the INFERYS prediction models are calibrated to best suit the experimental data. In the main search, CHIMERYS tries to best explain the experimental spectrum with the fewest peptides required, deconvoluting the potentially chimeric experimental spectrum into multiple peptide spectral matches. In this process, CHIMERYS calculates a multitude of intensity-based scores that are subsequently sent to Percolator for the false discovery rate calculation. The results are then downloaded back to Proteome Discoverer as a list of PSMs.

The intelligent search engine CHIMERYS is developed by MSAID GmbH and distributed by Thermo Fisher Scientific.

Comet

Comet supports real-time search data from Thermo Scientific Obitrap Eclipse™. The Comet version is 2019.01. For more information on Comet, visit https://uwpr.github.io/Comet/.