FAQ ABOUT CHIMERYS

CHIMERYS is an intelligent, AI-powered search algorithm for bottom-up proteomic data analysis. The name "CHIMERYS" originates from its remarkable ability to deconvolute chimeric MS2 spectra, a frequent phenomenon in tandem mass spectrometry, where multiple peptides are co-isolated and co-fragmented due to similar physicochemical properties. CHIMERYS 2.0 is compatible with data-dependent acquisition (DDA), data-independent acquisition (DIA), and parallel reaction monitoring (PRM) data. CHIMERYS is implemented as a cloud-native service and is integrated into Thermo Scientific™ Proteome Discoverer™ 3.1 Software.

CHIMERYS leverages the power of accurately predicted peptide properties, which are obtained from the deep-learning framework INFERYS™. CHIMERYS utilizes predicted spectra to best explain the experimental MS2 spectrum with the fewest candidates possible. This way, the algorithm deconvolutes the experimental intensities and derives the contributions for all peptides in the MS2 spectrum. This enables CHIMERYS to identify multiple peptides in chimeric MS2 spectra. The algorithm operates in a spectrum-centric manner and is fully compatible with MS2 spectra from various acquisition methods.

CHIMERYS 1.0 was introduced in 2022 and released as part of Proteome Discoverer 3.0. CHIMERYS 1.0 is compatible with DDA data only. In 2023, we unveiled CHIMERYS 2.0, which is integrated into Proteome Discoverer 3.1 and supports the analysis of data data-dependent acquisition (DDA), data data-interdependent (DIA), and parallel reaction monitoring (PRM) data, providing you with an unifying data analysis solution for all popular proteomics data acquisition types.

CHIMERYS 2.0 is implemented as a subscription-based cloud service. Thermo Fisher Scientific hosts the CHIMERYS service using Amazon Web Services on servers physically located in Ireland. While new servers will be added in other geographies, our European customers will continue to use the servers in Ireland. The CHIMERYS node in Proteome Discoverer extracts the MS/MS spectra from .RAW files and sends them along with a .FASTA file to the service for the search. All communication with the service is encrypted via HTTPS ensuring data security. The data may be queued as it is waiting for other CHIMERYS runs to finish depending on the type of subscription purchased. Once the CHIMERYS analysis is complete, the peptide identifications are securely transmitted back to Proteome Discoverer and the collection of MS/MS spectra and the FASTA file are deleted from the service. It is worth noting that .RAW files and .RAW file metadata are never transmitted to the service, ensuring the privacy and confidentiality of this data. 

CHIMERYS 2.0 is integrated into Proteome Discoverer 3.1 software. To learn more about licensing and obtain the software, please visit Proteome Discoverer page or get in touch with your local Thermo Scientific sales representative. You can also request a free Proteome Discoverer 3.1 and CHIMERYS 2.0 demo here.

You can request a free CHIMERYS 2.0 demo here or visit the Proteome Discoverer 3.1 page. We will send you login credentials with 24 hours of CHIMERYS processing time, which roughly translates to 24 hours of LC-MS/MS measurement time. If you need more time, please do not hesitate to reach out to us via info@msaid.de.

Proteome Discoverer 3.1 software comes with a subscription to the CHIMERYS cloud service. There are three subscription tiers available: Lite, Full and Plus. The difference between them is the number of daily compute capacity available on the CHIMERYS cloud service. For a detailed description of the subscription options and licensing information, please visit the Proteome Discoverer page or get in touch with your local Thermo Scientific sales representative.

CHIMERYS 2.0's capabilities are in part dependent on the capabilities of the deep-learning framework INFERYS™, which predicts peptide properties crucial for reliable peptide identification. CHIMERYS 2.0 is compatible with Thermo Fisher .RAW files and MS2 spectra derived from Orbitrap™, Ion Trap, or Orbitrap Astral™ mass analyzers. It supports the analysis of DDA, DIA, and PRM data of label-free or Tandem-mass tag™ (TMT6/10/11 and TMTpro) labeled peptides of length 7 to 30 amino acids. It supports a multitude of proteolytic enzymes, oxidized methionine and phosphorylated serine, threonine, and tyrosine residues as variable modifications and carbamidomethylated cysteine as a fixed modification. CHIMERYS 2.0 is not compatible with crosslinked peptides and glycopeptides.

Setting up a CHIMERYS in the Proteome Discoverer Software is a straightforward process that can be completed in two easy steps: Step 1: Download and install the Proteome Discoverer 3.1 software demo. Step 2: Log into the CHIMERYS service using the provided credentials. For detailed guidance on setting up the CHIMERYS demo, you can download the CHIMERYS Demo Installation guide from here.

Configuring a CHIMERYS search within the Proteome Discoverer Software is a simple and user-friendly task. If you'd like a step-by-step visual walkthrough on how to set up a CHIMERYS search job, we've prepared an informative video tutorial that you can access by clicking here.

If you encounter any difficulties or have any questions, our support team is always here to help you. Feel free to reach out for any assistance you may require.

The answer to this question depends on the data analyzed. For MS1-based quantification, CHIMERYS does not perform its own quantitation but utilizes the Minora Feature Detector Node in Proteome Discoverer Software. For MS2 Reporter ion-based quantification (i.e., TMT-based quantification), the Reporter Ion Quantifier Node in Proteome Discoverer is used. For MS2 fragment ion-based quantification as used in DIA or PRM data analysis, CHIMERYS calculates a quantification value by tracing the contribution of a peptide to a series of spectra along the retention time dimension. This value is imported into Proteome Discoverer by the Fragment Ions Quantifier Node.

Which PTMs can be analyzed with CHIMERYS depends on the capabilities of the deep-learning framework INFERYS™ that predicts peptide properties used for the identification of peptides. Currently, CHIMERYS is compatible with methionine oxidation and phosphorylation. We have received multiple requests for the addition of other common PTMs like acetylation, ubiquitination, methylation, etc. and our team is working hard to make them available as soon as possible. 

Yes, CHIMERYS 2.0 is compatible with ion-trap-data generated using HCD or CID fragmentation. While CHIMERYS profits from high-resolution accurate mass (HRAM) spectra, we have seen that CHIMERYS consistently outperforms traditional search engines on ITMS data as well. However, there are some tricks to improve the analysis: we advise to use as narrow MS2 fragment tolerances as possible (e.g., 0.25 Da or 0.3 Da instead of 0.5 Da). Second, we recommend to use peak filters in the Proteome Discoverer processing workflows for ITMS data. Here, a Top10/Top15/Top20 by 100 Da filter node before the CHIMERYS workflow can help to improve sensitivity and identification rates by removing peaks with low information content from the spectrum before the search. 

CHIMERYS employs a data-driven calibration step during the search. If the initial search does not yield enough high-scoring identifications, CHIMERYS cannot calibrate itself to the data and will stop the calculations. Frequently, this is observed when the chosen settings (e.g., modifications, labels or tolerances) or FASTA file do not match the .RAW file (e.g., wrong MS2 tolerance for the analyzer). Please double-check your settings before opening a support ticket at pd.support@thermofisher.com.

Currently, CHIMERYS 2.0's data analysis is limited to Thermo Scientific instruments that write the .RAW format. This includes all Thermo Scientific Orbitrap, ion trap, and Orbitrap Astral mass spectrometers.

We constantly test and monitor the compatibility and performance of the CHIMERYS service. However, in rare cases, CHIMERYS might not perform as expected. If you encounter an issue with CHIMERYS that cannot be attributed to incorrect settings or a broken .RAW file, please open a ticket with pd.support@thermofisher.com. In order to quickly follow up with the search you attempted, please extract the FULL CHIMERYS JOB ID from the Proteome Discoverer Log file (setting Verbose switched on) and communicate this ID to the support staff.

With CHIMERYS 2.0 in PD 3.1, there's no longer a need to link the Percolator node to the CHIMERYS node. This is because the FDR (False Discovery Rate) estimation is automatically conducted in the cloud. For a faster processing experience, we've replaced the Percolator algorithm with the reimplementation termed. Therefore, there's no requirement for you to include the Percolator node manually.

Currently, Proteome Discoverer is used as a client to interface with the CHIMERYS cloud-service or a local server solution running CHIMERYS. However, we are actively developing a stand-alone version of CHIMERYS, allowing you to utilize it without the need for Proteome Discoverer. This stand-alone version will be available as a Software-as-a-Service (SaaS) product. We are excited about this development and will share more details as we approach the release. If you want to stay up-to-date on these developments, feel free to subscribe to our newsletter here. 

Your feedback and feature requests concerning CHIMERYS are highly valuable to us. Please feel free to share your thoughts and suggestions with us at info@msaid.de. For feedback and feature requests specific to the Proteome Discoverer software, please get in touch with pd.support@thermofisher.com.