Sample Prep

Forma 1800 series Clean Bench

The Thermo Scientific* Forma 1800 clean benches provide a Class 100 work area for procedures requiring a particle-free environment. The horizontal laminar airflow clean bench creates a filtered-air environment which reduces contamination, such as keratins, during sample preparation.

ProGest Protein Digestion Station and SPD SpeedVac

The ProGest Protein Digestion Station (Genomic Solutions®) is an automated system for in-gel and in-solution digestion of proteins for LC-MS/MS analysis. All washing, reduction, alkylation and enzymatic digestion steps are automatically performed using programmable temperature incubation cycles. The Methods Editor software allows complete control of every step, so specific programs can be tailored for challenging samples. This fully automated and enclosed system avoids cumbersome manual work and reduces external sources of contamination, such as skin keratins.

The SPD111V (Thermos Savant) vacuum concentrator is used for concentration or drying of biological and non-biological materials in all kinds of solvents. This device is consists of a concentrator, a vapor trap and a vacuum pump and is suitable for molecular biology applications. Peptide extracts are typically concentrated and/or dried-up prior to MS analysis to improve the levels of detection and remove volatile interferents.

AKTA Pure Fast Purification Liquid Chromatography system

The AKTA Pure (GE Life Sciences) is a preparative liquid chromatography system for fast and easy purification of proteins and peptides. This system is used as the first dimension of separation in a typical 2D-LC method where peptides are separated into fractions using strong cation exchange chromatography, prior to LC-MS/MS analysis.

ÄKTA pure is a flexible and intuitive chromatography system for fast purification of proteins, peptides, and nucleic acids from microgram to gram levels of target product.

  • Modular system design with a large range of options to allow flexibility in purification of proteins and peptides.
  • Customizable system that is easy to upgrade as your research needs develop.
  • Reliable system with components and integrated features based on the proven design of ÄKTA avant.
  • UNICORN software simplifies your work by providing simple, intuitive, and flexible total system control including drag-and-drop method creation.

Visiprep Solid Phase Extraction Vacuum Manifold

Visiprep™ Solid Phase Extraction Vacuum Manifold automates the preparation and cleanup of laboratory liquid samples by solid phase extraction. This step is critical for the removal of interfering chemicals, desalting and concentrating protein/peptide samples into MS compatible solvents. Used with a vacuum pump, a Visiprep manifold can extract up to 12 samples simultaneously, significantly increasing sample throughput while decreasing sample preparation hands-on time. Flow control valves can precisely manipulate flow through each tube and the disposable valve liners virtually eliminate contamination from one sample to the next.


Q-Exactive Orbitrap (Thermo Scientific)

The Thermo Scientific Q Exactive hybrid quadrupole-Orbitrap mass spectrometer combines high-performance quadrupole precursor selection with high-resolution, accurate-mass (HR/AM) Orbitrap™ detection. The Q Exactive™ MS/MS data provides a wide range of qualitative and quantitative applications. Its high scan speed and spectral multiplexing capabilities make it fully compatible with UHPLC and fast chromatography techniques. This instrument is currently connected in-line to a Vanquish UHPLC system and being used for metabolomics and lipidomics workflows.

VelosPRO Orbitrap (Thermo Scientific)

The VelosPRO provides ultra-high resolution (maximum resolution > 100,000 at m/z 400) and accurate mass acquisitions (< 1 ppm RMS using internal calibration) for confident structural elucidation. Powered by Orbitrap technology, this high mass accuracy system increases the confidence of peptide identification in com­plex samples by minimizing false positive identification. This systems can perform collision induced dissociation (CID), high energy collisional dissociation (HCD) and electron transfer dissociations (ETD). In combination, these fragmentation modes provide extensive structural information for peptide identification and post-translational modification studies. Precise intact protein analysis, rapid quantitation of low level isobarically-labeled peptides and multiple fragmentation techniques can all be performed in this a single instrument.

QTRAP® 5500 with SelexION ion mobility source (Sciex)

The Qtrap5500 LC/MS/MS system (AB SCIEX) is designed to excel at detection and confirmation of low-level analytes, and can be specifically used for quantification, verification and validation of  protein/peptide biomarkers. The QTRAP® 5500 system houses a linear ion trap with ultra-fast scan speeds of up to 20,000 Da/s. The flexibility of this system allows a variety of acquisitionmodes, including high-sensitivity full-scan MS, MS/MS, and MS3 capabilities. High-selectivity can be achieved from true triple quadrupole precursor ion (PI) and neutral loss (NL) scans. Accurate and precise quantitation can be obtained by selected reaction monitoring (SRM, also known as Multiple Reaction Monitoring, MRM) using the high-sensitivity triple quadrupole configuration. Furthermore, the QTRAP 5500 is equipped with a differential ion mobility source. This novel SelexION™ Technology device delivers a new dimension of selectivity and performance for applications requiring the separation of isobaric species, elimination of challenging co-eluting contaminants and reduction of high background noise.

Dionex Ultimate3000 RSLC-nano Systems

Both the VelosPro and the QTRAP 5500 MS/MS systems are equipped with two new liquid chromatography systems manufactured by DIONEX, a company which has pioneered the science of chromatography. These LC systems deliver can deliver flows from 20 nL/min to 10 mL/min and handle a wide range of operating conditions, including ultra high pressure (UHPLC) nanoflow separations, critical for applications in the area of proteomics.

Vanquish UHPLC

Thermo Scientific Vanquish UHPLC was designed from the ground up to improve performance and repeatability with no trade-offs in quality, robustness, or ease of use. Vanquish Flex excels from method development to routine analyses. With a quaternary pump, the Vanquish Flex offers outstanding performance for targeted LC and LC-MS workflows.

Agilent 1100 HPLC

The Agilent 1100 is a robust HPLC system that is interfaced to our MS/MS systems for high flow targeted metabolomic and proteomic workflows. It is equipped with an autosampler, a degassing unit and a quaternary pump module.   


Analyst 1.5

Analyst 1.5 allows the visualization, interpretation and annotation of MS spectra obtained from the QTRAP 5500 and 2000

BioAnalyst Software

BioAnalyst Software is a comprehensive, fully integrated set of data processing tools within Analyst® Software for the identification and characterization (e.g. post-translational modifications) of peptides and proteins using mass spectrometry data. These tools include reconstruction of MS data for automated molecular weight determination and a de novo sequencing algorithm for automated sequencing of peptides from unknown proteins.


Xcalibur software is a flexible Windows-based data system that provides instrument control and data analysis for our VelosPRO LC-MS/MS instrument.

Proteome Discoverer 2.1

Thermo Scientific Proteome Discoverer software is a flexible, expandable platform for the analysis of qualitative and quantitative proteomics data. Outstanding sensitivity and the rapid growth of public databases have made mass spectrometry the primary method of identifying proteins in complex biological samples. Proteome Discoverer was designed to address this need for flexibility by offering a wide array of bio-software tools and customizable workflows for every proteomics experiment.


SIEVE is an automated solution for the label-free, semi-quantitative differential expression analysis of proteins, peptides and metabolites. SIEVE performs differential analysis of sample populations, comparing LC/MSn spectra to find differentially expressed features. Using SIEVE software to pre-filter data greatly reduces the number of compounds that need to be identified, significantly increasing the throughput of complex biomarker discovery experiments. Combining SIEVE software with the unique analytical power of Thermo Scientific LC/MS systems creates complete solutions for biomarker discovery.

TransProteomicPipeline (TPP)

The TransProteomicPipeline is an integral platform for MS/MS-based shotgun proteomics analysis with a well-established worldwide user community. The TPP allows conversion of raw data into open formats and performs peptide database searching with X!Tandem search engine. Furthermore, it includes a statistical validation and quantification module for the identified peptides and proteins.


Skyline is a Windows client application is used for building MRM quantitative methods and analyzing the resulting mass spectrometer data. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies.


Multiple reaction monitoring (MRM) experiments have emerged as the definitive analytical tool for drug quantitation in pre-clinical and clinical trials. More recently, the proteomics market has started adopting MRM assays for monitoring proteins and peptides in biological samples for applications such as biomarker verification/validation, post-translational modification characterization, pathway mapping, and other targeted quantitative proteomics applications. MultiQuant Software is a powerful and easy-to-use quantitation package that processes MRM data for quantitative information. The software enables you to process many analytes and samples at the same time, with an emphasis on the requirements for processing protein/peptide quantitative workflows.


PepNovo is a bioinformatic tool that allow 'de novo' peptide sequencing from MS/MS data that does not require any knowledge of the sequenced genome (database).