Run & Done with PaSER

PaSER 2022

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



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.
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 PaSER’s smarts will make sure they are not wasted needlessly.
Instrument time, reagents and sample preparation are costly. PaSER and Run & Done will save money because you are assured you are producing meaningful data.


PaSER 2022

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


  • CCS-aware 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
  • 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


PaSER 2022

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.


PaSER 2022

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 PTM studies, becomes reality.

See what you have always been missing

现代艺术博物馆观众由蒂姆斯即提供电力ful ability to view 4D-Proteomics data like never seen before. The mobility separation and focusing upstream from the quadrapole and TOF results 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 before.




“Real-time results delivered by the PaSER 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.“

塞巴斯蒂安弗吉尼亚州ca, PhD, Research Scientist, Proteomics Platform at the Broad Institute of MIT and Harvard (Carr Lab), Cambridge, USA

“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.”

Professor John Yates III, the Ernest W. Hahn Professor at The Scripps Research Institute in La Jolla, California