Over $10M invested in instrumentation

We provide highly accurate data for biological research via
protein mass spectrometry and proteomics.

Instrumentation

MS Bioworks uses ThermoFisher Orbitrap platforms  with nanoscale liquid chromatography systems for all projects. This is industry leading instrumentation employed by many academic thought-leaders. We currently have, one Orbitrap-Astral, two Orbitrap Fusion Lumos, two Exploris 480 and one Q Exactive mass spectrometers.

The Orbitrap Astral Mass Spectrometer

The Orbitrap Astral Mass Spectrometer combines three mass analyzers: a quadrupole mass analyzer for high selectivity and high ion transmission; an Orbitrap mass analyzer for high dynamic range and high-resolution measurements; and a novel Astral analyzer for fast and sensitive measurements.

The front end, from the ion source up to the segmented quadrupole mass filter, is designed to maximize instrument sensitivity and robustness.

Ions are trapped and concentrated in the ion routing multipole, which facilitates the transfer of ions to either of the high-resolution accurate-mass (HRAM) analyzers. Synchronization of ion transfer and processing throughout the instrument enables the parallel handling of five separate ion packets simultaneously. This synchronization enables each mass analyzer to be used in combination to optimize performance and experimental flexibility.

High Acquisition Rates and Range

The Astral Mass Analyzer delivers high acquisition rates up to 200 Hz, single ion detection sensitivity, and high dynamic range HRAM, SIM, and MS2 measurements that are fully synchronized with parallel Orbitrap analyzer operation.

Exceptional data acquisition

The Orbitrap Astral Mass Spectrometer excels at many data acquisition strategies including High Resolution Data-Independent Acquisition (HR-DIA) and data-dependent acquisition (DDA).

accurate and precise quantitation

Capable of accurate and precise quantitation using either Label-Free Quantitation (LFQ) or multiplexing with Tandem Mass Tag (TMT)-labeled peptides.

The Orbitrap Exploris 480

This mass spectrometer has unique capabilities which impart extra speed, depth, and certainty to enable you to run more experiments or to gain deeper insights into your research.

It facilitates a broader range of experiments with multiple scan modes: data-dependent acquisition (DDA), data independent acquisition (DIA), spectral multiplexing (MSX), TopN and new TopSpeed (TopS), BoxCar DIA and DDA experiments, tSIM, tSIM MSX, ddMS/MS, targeted MS/MS

Instrument performance highlights include:

480,000

Max Resolution

40Hz

Max Scan Speed

40-8000

M/Z Mass Range

>5000:1

Dynamic Range

Orbitrap Fusion Lumos Tribrid

Our Orbitrap Fusion Lumos Tribrid mass spectrometers are the industry-leading high-performance mass spectrometers. Our systems are equipped with HCD, CID and ETD fragmentation.

Tribrid architecture

Includes quadrupole mass filter, linear ion trap and Orbitrap mass analyzers Ultrahigh resolving power up to 500,000 FWHM

Full parallelization of MS and MSn

Enable simultaneous execution of MS and MSn analyses, ensuring unparalleled efficiency and comprehensive data acquisition

Synchronous Precursor Selection

For MS and MSn experiments, significantly increasing the number of peptides and proteins identified and improves quantitative accuracy when using isobaric mass tags.

Flexibility of fragmentation

CID, HCD, ETD and EThcD available at any stage of MSn

Q Exactive

Our Q Exactives are hybrid quadrupole-Orbitrap mass spectrometers, ideal for discovery proteomics, quantitative proteomics, and PTM-related work. Featuring high-performance quadrupole mass filters and the industry-leading high-resolution Orbitrap mass analyzer, this instrument also incorporates a quadrupole mass filter and combines spectral multiplexing for an enhanced duty cycle with an S-Lens ion source for increased sensitivity.

Identify, quantify and confirm with unmatched confidence using the Q Exactive mass spectrometer.

140,000

Max Resolution POWER

12hz

Max Scan Speed

>5000:1

DYNAMIC Range

Data Analysis

MS Bioworks uses Mascot, Scaffold, MaxQuant, Perseus, Byonic and Skyline packages for data processing and review.

MS Bioworks uses the Mascot database search engine to identify proteins from primary sequence databases. Mascot is developed and distributed by Matrix Science Ltd, to find out more about how Mascot enables the confident identification of peptides and proteins from complex LC-MS/MS datasets visit the Matrix Science homepage here.

MS Bioworks uses the Scaffold data processing software to visualize and mine database search results. Our clients can view their data using the free Scaffold viewer appropriate for their operating system. Scaffold is developed and distributed by Proteome Software, for more information about Scaffold and the option to download the free data viewer visit the Proteome Software website here.

MS Bioworks is using Protein Metrics Byonic software to expand our glycoproteomics and PTM identification and localization workflows. For more information on Byonic and their new approach to database searching for the identification of modified peptides and proteins visit the Protein Metrics website.

MaxQuant and Perseus are quantitative proteomics tools for analyzing large scale mass spectrometric data sets. MaxQuant with the Andromeda search engine enables protein identification and quantitation. Perseus enables statistical analysis of the MaxQuant output. You can find out more about MaxQuant here.

DIA-NN – a universal software for data-independent acquisition (DIA) proteomics data processing by Demichev, Ralser and Lilley labs. In 2018, DIA-NN opened a new chapter in proteomics, introducing a number of algorithms which enabled reliable, robust and quantitatively accurate large-scale experiments using high-throughput methods. For more information access the DIA-NN website here.

CHIMERYS is an intelligent, AI-powered search algorithm for bottom-up proteomic data analysis. The name “CHIMERYS” originates from its remarkable ability to deconvolute chimeric MS2 spectra, a frequent phenomenon in tandem mass spectrometry, where multiple peptides are co-isolated and co-fragmented due to similar physicochemical properties. CHIMERYS 2.0 is compatible with data-dependent acquisition (DDA), data-independent acquisition (DIA), and parallel reaction monitoring (PRM) data. CHIMERYS is implemented as a cloud-native service and is integrated into Thermo Scientific™ Proteome Discoverer™ 3.1 Software. You can find out more about CHIMERYS here.

Proteome Discoverer software simplifies a wide range of proteomics workflows, from protein and peptide identification to PTM analysis to isobaric mass tagging and both SILAC and label-free quantitation. It supports multiple database search algorithms and multiple dissociation techniques. Go beyond searching to discovering with intelligent INFERYS™ Rescoring and the CHIMERYS™ intelligent search algorithm by MSAID to substantially increase the number of unique peptide identifications. Discover more about Pd here.

Skyline is a freely-available and open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), Data Independent Acquisition (DIA/SWATH) and DDA with MS1 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 quantitative mass spectrometry studies in life sciences. Learn more about Skyline here.