PepSep Columns
PepSep Columns

PepSep™ Columns & Emitters

Everything you need for PASEF® speed

HPLC Columns for Mega-sensitivity, High Throughput, and Maximum Reproducibility

High-performance liquid chromatography (HPLC) reversed phase columns are crucial components that determine the degree of separation in every analysis. In the world of proteomics, unlocking separation with precision can help with the quality of your analysis. 

Scientists, researchers, and clinicians desire robustness, speed, and sensitivity from their HPLC and mass spectrometry (MS) systems. Having a system that can accommodate large sample cohorts with minimal maintenance during chromatographic separation is a desirable trait to ensure sample reproducibility. The key to optimizing the chromatography process starts with columns. Having the right chromatographic column will assist in accurate data collection, reproducible results while offering higher throughput, and sensitivity.


This is where columns and tips are critical:
   (a) Bridging the gap between liquid chromatography (LC) and MS
   (b) Retaining peptides/ binding to active sites
   (c) Chromatographic resolution

omg OMx Podcast

omg OMx Podcast Episode 5 with Balyn Zaro

Tune in omg OMx Podcast where Dr. Balyn Zaro talks about PepSep and more.

Flow with PepSep™

PepSep™ C18 columns are the preferred columns in academic and core labs that are focused on speed, reproducibility and sensitivity. Easily connect columns to nanospray sources with a simple twist on and twist off design.

PepSep™ HPLC columns are perfect for all proteomics applications. These columns are designed for high-throughput applications and offer superior sensitivity and resolution. With a diverse portfolio of nanoflow columns featuring various lengths, inner diameters, and particle sizes, rest assured with industry leading materials and connections to accommodate all chromatographic separation needs.

Spend less time swapping columns and more time on the important things, results. Amplify your experience when you combine PepSep™ consumables with timsTOF series instruments, powered by Bruker ProteoScape™ to enhance your ability to acquire data at PASEF® speeds. 

"We are truly amazed by the performance of PepSep columns, which have become indispensable for us in achieving remarkable high-throughput proteomics.

Working seamlessly alongside our Bruker timsTOF Pro mass spectrometer, PepSep columns enable us to utilize higher nanoflow rates with minimal back pressure elevation. This translates to quicker analysis times and a substantial boost in sample throughput. "

David Gómez-Varela, Ph.D., Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria

The Best Column for Your Needs

Ultra power for spectral library generation, designed for longer gradients.

PepSep™ MAX HT
Maximize speed, resolution and dynamic range.

Ultra-high sensitivity and reproducibility at PASEF® speeds

Exceed sample throughput limits at PASEF® speeds with high 4D-sensitivity

PepSep™ MAX
Maximize performance to accurately analyze 1000s of samples

PepSep™ ULTRA XL: The Ultimate Spectral Library Generation Column

The PepSep™ ULTRA XL column (50 cm x 75 µm x 1.5 µm) is designed for long gradients, which are essential for spectral library generation. Spectral libraries play a crucial role in proteomics, particularly in mass spectrometry-based proteomics.

Different K562 concentrations were injected onto PepSep™ ULTRA XL column attached to the timsTOF HT coupled to the nanoElute 2 UHPLC. A standard DDA PASEF method, 1/k0 start 0.70, 1/k0 end 1.3 was used. results were searched using Bruker ProteoScape™ search engine.

PepSep™ MAX HT: A Short Column for High-Throughput Proteomics

Designed for high-throughput proteomics, the PepSep™ MAX HT (5 cm x 150 µm x 1.5 µm) allows for gradients less than 15 minutes. This makes it ideal for applications where speed is essential, such as the analysis of clinical samples or the screening of drug libraries.

Results of different K562 concentrations separated on the new PepSep™ MAX HT (5 cm x 150 µm x 1.5 µm) column. The column was coupled to the nanoElute® and timsTOF HT. Two short gradients, 5 minutes and 10 minutes were used. The dia-PASEF 6x3 method was used with the IM set at 0.6 1.k0 start and 1.4 1/k0 end. Results were searched with DIA-NN.

PepSep™ ULTRA: Enhance Sensitivity

Choosing the right column is difficult. A make-or-break decision that may increase protein and peptide identifications. The PepSep™ ULTRA (25 cm x 75 µm x 1.5 µm) C18 HPLC columns enable the analysis of a higher number of proteins and peptides from routine to restricted sample types. 

Based on the results from different digest concentrations of K562 run on the PepSep™ ULTRA column (25 cm x 75 µm x 1.5 µm) over a 60 minute gradient. The PepSep™ ULTRA column was coupled with nanoElute® and timsTOF HT using a 6x3 dia-PASEF® window scheme and Bruker ProteoScape™ to search the data in real-time.

PepSep™ XTREME: Greater Depth, Breadth and Rapid Proteomics

Core labs and academic labs want a single column solution for all applications to achieve deeper coverage, higher throughput, and better identification. 

PepSep™ XTREME (25 cm x 150 µm x 1.5 µm) will help increase instrument performance, allowing scientists the liberty to have both sample throughput at PASEF® speeds and high 4D-sensitivity to dive deeper into the unknown and open the potential of the plasma proteome. 

Results from PepSep™ XTREME (25 cm x 150 µm x 1.5 µm) columns on 45- and 60-min gradients with different K562 digest concentrations. PepSep™ XTREME was coupled with nanoElute® and timsTOF HT using a 6x3 dia-PASEF® window scheme and Bruker ProteoScape™ to search the data in real-time.

PepSep™ XTREME: Excellent Performance Driven by Enhanced 4D-Sensitivity

Rather than deciding between a shorter gradient and high throughput, PepSep™ XTREME C18 HPLC columns offer you the best of both worlds. It’s time to improve your proteomics analysis with better coverage, throughput, sensitivity, and reproducibility. Pair the PepSep™ XTREME with the timsTOF Pro 2 to find unprecedented proteomics depths — more than 5500 protein groups, 42,000 peptides in a 30 min gradient.

Using the nanoElute® UHPLC coupled to the timsTOF Pro, 200 ng K562 was run on the PepSep™ XTREME with the 5 mm Thermo Pepmap trap. In this experiment, the default short gradient DDA MS method was used. The data was analyzed using MSFragger.

PepSep™ MAX: Advancing Proteomics Research 

Scientists spend time fine tuning their methods to achieve broader coverage and higher throughput when mining plasma proteomes. 

The PepSep™ MAX (10 cm x 150 µm x 1.5 µm) increases instrument performance to help drive your analysis. When combined with the timsTOF HT, immerse yourself in 4D-Proteomics™, so you can accurately analyze 1000s of samples with high throughput at PASEF® speed.

PepSep™ MAX 20 min and 6 min: Precursors, peptides and protein groups identifications measured from healthy human donor plasma on the timsTOF HT. Plasma was prepared using the PreOmics iST-BCT kit. Peptide separation was performed on the nanoElute UHPLC coupled to the PepSep™ MAX column run over 5.8- and 20-min gradients. 200 ng were injected for both gradients. Spectronaut 18 with directDIA+ was used for data analysis. 
DDA and DIA results of 200 ng commercial HeLa digest run on 50 samples per day (17.8 min gradient) using the PepSep™ MAX column attached to timsTOF HT.  For dia-PASEF®, a 6x3 windows scheme was used. Data results were generated in Bruker ProteoScape™ search engine.

Analyze More Samples, in Less Time, with Better Reproducibility

The proteomics landscape requires high throughput to capture meaningful rich data. PepSep™ MAX columns help you get there. It's time to improve your HPLCs capabilities. 

Identify, characterize and quantify peptides and proteins. Get excellent reproducibility, while outlasting leading columns up to 2x longer.

"At first, we were just using PepSep™ columns on our Bruker timsTOF Pro mass spectrometer. But we have been so impressed with their performance and affordable price point that we now use them across all instruments in our lab.  


These columns really hit a sweet spot of top-notch chromatography but with minimal back pressure. When compared to traditional nanospray columns, this allows us to use higher flow rates and minimize LC overhead time. This has been crucial for throughput, particularly when thousands of samples using shorter gradients."  

Danielle Swaney, Assistant Professor, Cellular Molecular Pharmacology, University of California, San Francisco, USA

When Performance Meets Simplicity 

Plug and play ready-to-use emitters are equipped with column connection union and spray tip to facilitate a hassle-free CaptiveSpray setup.

With two IDs available, PepSep™ emitters cover the unique demands of proteomics applications. Compatible with all CaptiveSpray Sources.

Related Information


For Research Use Only. Not for use in clinical diagnostic procedures.