Break the data analysis bottleneck by integrating real-time database search and smart acquisition provided by Bruker ProteoScape™.
Massive parallelization with GPU power
Bruker ProteoScape™ data review
“Innovative software tools are a necessity to address unanswered biological questions with mass spectrometry. The trapped ion mobility functionality and the robustness of the timsTOF Pro offer unique bottom-up proteomics capabilities that can be effectively used to study many diseases.”
TIMScore™ provides the greatest number of PSM, peptide and protein identifications by enabling the CCS dimension for true 4D-Proteomics.
The Bruker ProteoScape™ search algorithm is run as normal, combined with comparison of the predicted and measured CCS values and calculating a TIMScore™ for the top 5 peptide candidates for each spectra.
The TIMScore™ benefit is realized during the peptide-validation and False Discovery Rate (FDR) estimation steps. In a non CCS-enabled algorithm, only two dimensions can be utilized to estimate the FDR rate, and so a discriminate line is fit to a 1% error (Panel A) to distinguish forward and reverse peptide candidates. With TIMScore™, and the extra CCS dimension, the peptide-candidates can be vectorized in 3 dimensions (Panel B) allowing a discriminate contoured plane to be applied to achieve the same 1% error.
Applying a discriminate plane provides increased accuracy and precision, helping to validate formerly poorly scoring PSMs in the standard two dimensions.
To further discoveries in immunopeptidomics, metaproteomics and other applications where de novo sequencing is needed, we developed BPS Novor together with Rapid Novor Inc.. Our solution provides the quickest, most accurate de novo sequencing results for timsTOF data with all the advantages of Run & Done.
BPS Novor was trained and optimized on greater than >1,780,000 spectra from the timsTOF platform including a variety of non-tryptic enzymes, to build a generalized scoring model. It is capable of processing on average >1000 spectra/second, lending itself for real-time de novo sequencing on the timsTOF platform. BPS Novor consistently outperforms standard Novor and Software A on a variety of datasets.
BPS Novor does not show a noticeable bias for digestion specificity or species and is 20x faster than competing products.
Combined with PASEF technology on the timsTOF platform, Bruker ProteoScape™ and BPS Novor provide enhanced sensitivity for real-time de novo sequencing for a variety of applications including immunopeptidomics.
“De novo searches have been a critical aspect in my labs research for many years, the ability to have an algorithm that delivers results with accuracy and precision at the speed of acquisition means we can assess immunopeptidomics samples at scale and in real time. This has major implications in how fast my group can translate research findings into actionable information, and it pushes this workflow ever closer to delivering clinical impact of these analyses on an unprecedented timescale.”
Bruker ProteoScape™ is capable of processing dia-PASEF® workflows utilizing a customized version of the popular DIA-NN (DIA by Neural Networks) software from the Lilley, Rasler and Demichev labs. TIMS DIA-NN enables reliable, robust, and quantitatively accurate large-scale experiments. Bruker ProteoScape™ utilizes the same stream mechanism for dia-PASEF® workflows, streaming in real-time MS and DIA frames from the acquisition PC to the Bruker ProteoScape™ box. These dia-PASEF® data are processed and stored on the Bruker ProteoScape™ box. At the end of the acquisition a spectral library search is triggered, and the results recorded. TIMScore™ powered DDA search results can be easily utilized to build spectral libraries or spectral libraries can be imported from other popular tools. At the end of the project the users can trigger match-between-runs analysis to view a quantitative profile across projects. This provides users an integrated environment for PASEF® and dia-PASEF® data analysis.
"Our ongoing collaboration with Bruker to tailor DIA-NN to a streamlined processing tool for dia-PASEF data with a CCS focus has been really rewarding. It simplifies and accelerates identifying and quantifying thousands of proteins in even very short gradients. We are pleased that within our close collaboration with Bruker, the vendor-integrated version of DIA-NN called TIMS DIA-NN now becomes part of the Bruker ProteoScape bioinformatics platform."
Blazing search speed with uncompromised search results.
A) Protein ID from replicate DDA runs of a human cell lysate using Bruker ProteoScape™ for real-time results and benchmarked against MaxQuant
B) Peptide ID from replicate DDA runs of a human cell lysate using Bruker ProteoScape™ for real-time results and benchmarked against MaxQuant
C) Bruker ProteoScape™ and MaxQuant identify 97% of the same proteins and nearly 90% of the same peptides.
Bruker ProteoScape™ provides consistent results obtained from the real-time search, identical to offline search of the same data. Since the database search algorithm is run on the GPU, the search times are negligible compared to CPU based searches.
In addition to real-time search the opportunity to search a larger space for specific applications, including peptidome studies, becomes reality. Bruker ProteoScape™ benchmarked against the gold standard in DDA searches performs as good or better.
Take advantage of the real-time identification to drastically reduce the required time for dda-PASEF label-free quantitation (LFQ) with match-between-runs (MBR).
Easily identify poor samples and re-acquire them with Run & Done on Bruker ProteoScape™ before starting the quantitative portion of your workflow. Our IM filtered XIC based quantitative workflow is powered by the Census algorithm (https://doi.org/10.1002/0471250953.bi1312s29).
“Real-time results delivered by the Bruker ProteoScape box on our timsTOF Pro has been a huge time saver. This allows us to develop methods in real-time, inform on LC and instrument performance and overall a major gain in efficiency.“
For Research Use Only. Not for use in clinical diagnostic procedures.