PaSER

PaSER 2022 is a GPU powered real-time database search platform providing parallel computing power and real-time database search results for bottom-up proteomics.

 

Immediate Results | Real-time results – efficiency

TIMScore provides the greatest number of PSM, peptide and protein identifications by enabling the CCS dimension for true 4D-Proteomics.

The PaSER 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. With TIMScore, and the extra CCS dimension, the peptide-candidates can be vectorized in 3 dimensions allowing a discriminate contoured plane to be applied to achieve the same 1% error. 

PaSER
Bruker Daltonics

PASER IS EFFICIENCY AND SAVINGS

Real-time results inform you of current instrument and sample status

Analysis Time

Database searches take time, eliminate this step with uncompromised search results as soon as the acquisition is complete.

Instrument Time

Be sure every minute counts, with PaSER you can be assured that your instrument time is spent in the most meaningful way.

Precious Samples

Save those precious samples! Whether they are single cell, clinical, SILAC or enriched PTMs; PaSER’s smarts will make sure they are not wasted.

Costs

Instrument time, reagents and sample preparation are costly. PaSER and Run & Done will save money because you are assured you are producing meaningful data.

Important Features to Consider

4D-Proteomics™ with real-time search results and smart acquisition

Break the data analysis bottleneck by integrating real-time database search and smart acquisition provided by PaSER

Universally available

  • All current and future timsTOF Pro and fleX platforms are PaSER accessible

4D-Proteomics™

  • CCS-enabled data is rich, even so real-time database search capabilities are a reality with PaSER including with PTMs like phosphorylation

Massive parallelization with GPU power

  • PaSER is GPU powered, provides massive compute power across thousands of CUDA cores

PaSER Data Review

  • View the intricate details of your data from the high level experimental information to a specific fragment ion spectrum of interest with confidence from the integrated viewer onboard of all PaSER boxes

Smarts

  • PaSER is smart, where a user defined qualification of proteins or peptides at the end of a sample acquisition determines the progression of your sample queue, this checks suitability, save precious samples, expensive consumables and instrument time

Benefits

Benefit from time and cost savings

  • No more worrying about injecting those precious samples.
  • No more worrying of wasted instrument time.
  • No more worrying about those samples with expensive reagents and sample prep, only to inject on a poor performing system.
  • No more waiting for the QC runs to determine system suitability.
  • No more waiting for search results during method development.

Applications

TIMScore™ – Machine Learning and CCS exploited for better FDR

TIMScore provides the greatest number of PSM, peptide and protein identifications by enabling the CCS dimension for true 4D-Proteomics.

The PaSER 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.

dia-PASEF workflows streamlined on PaSER with TIMS DIA-NN

PaSER 2022 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. PaSER utilizes the same stream mechanism for dia-PASEF workflows, streaming in real-time MS and DIA frames from the acquisition PC to the PaSER box. These dia-PASEF data are processed and stored on the PaSER 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.

Y-axis are counts and X-axis is total K562 peptide loaded on column in nanograms. The gradient length was 35 minutes, supporting 30 samples per day with all experiments performed on a timsTOF Pro 2.

Full-fledged database search in less than 5 ms

Blazing search speed with uncompromised search results.

  • A) Protein ID from replicate DDA runs of a human cell lysate using PaSER for real-time results and benchmarked against MaxQuant
  • B) Peptide ID from replicate DDA runs of a human cell lysate using PaSER for real-time results and benchmarked against MaxQuant
  • C) PaSER and MaxQuant identify 97% of the same proteins and nearly 90% of the same peptides.

PaSER 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 including peptidome studies, becomes reality. PaSER benchmarked against the gold standard in DDA searches performs as good or better.

See what you have always been missing

TIMS Viz provides the powerful ability to view 4-D proteomics data like never seen before. The mobility separation and focusing upstream from the quadrapole and TOF result in the separation of isobaric and near isobaric species. Using other technologies and in the case of PTM enrichments and the analysis of complex samples it is common that co-eluting species that are isobaric or near isobaric in mass co-fragment. The timsTOF Pro/flex obviates this by first separating ions by their collisional cross section. The ability to visualize, search and sort on such events has never been available before. We term isobaric masses with different mobility values mobility offset mass aligned (MOMA), and TIMS Viz can tease such events out within complex runs. TIMS Viz allows you to set tolerances to your discretion while simultaneously overlaying both features and PSMs that were observed post database search. TIMS Viz enables you to view what you never knew was there before.

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