Run & Done with PaSER

PaSER 2023

PaSER 2023 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

Punti salienti

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.
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 2023

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-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
  • 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 2023

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 2023

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.

PaSER 2023

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

PaSER 2023 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.

"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 PaSER bioinformatics


Prof. Dr. Markus Ralser, Einstein Professor of Biochemistry at Charité, Berlin, Germany

PaSER 2023

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.

PaSER 2023

Saves HOURS on LFQ workflow with real-time aided ID

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).

  • Uses TIMScore for CCS enhanced IDs
  • Typically, 1/20th acquisition time to perform quant
  • SAVE massive amounts of time using PaSER

Easily identify poor samples and re-acquire them with Run & Done on PaSER before starting the quantitative portion of your workflow. Our IM filtered XIC based quantitative workflow is powered by the Census algorithm (

Project # of Samples MS acquisition Length (min) Total Acquisition Time (min) LFQ Processing Time (min) Ratio vs Acquisition
Test 2 13.33 26.66 1.25 1/21
Dense HE Data 6 40 240 26.2 1/9
Tenzer style HYE124 6 120 720 24.5 1/30
Human Ecoli spike 18 40 720 116.8 1/6
HYE Dilution 4 120 480 13.1 1/37
Plasma App Note 212 14.4 3052.8 59.6 1/50
PaSER 2023

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.


PaSER 2023



“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.“

Sebastian Vaca, 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

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