Global Quantitative & Qualitative Profiling
Quadrupole Orbitrap MS/MS : Thermo Q-Exactive with nUPLC 
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 superior quality of Q Exactive™ MS/MS data provides ultimate confidence for 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, ramping roductivity to a new level.
The Q Exactiveinstrument can easily handle routine applications in proteomics from bottom-up protein ID to semiquantitative isotopic labeling analyses to targeted quantification experiments. At the same time, its innovative HR/AM Quanfirmation™ capability makes the Q Exactive mass spectrometer the ideal solution for fast, easy residue screening and quantification in food safety, environmental and toxicology labs. The Q Exactive MS is superbly suited to routine bioanalytical quantitation of both large and small molecules; the superior quality of its HR/AM data supplying an added degree of confidence to these analyses. It is also ideal for pharmaceutical research laboratories looking for confident ID and precise quantification of metabolites, impurities, leachables and extractables. In short, the versatility and high data quality of the Q Exactive LC-MS/MS system make it a valuable addition to any modern laboratory.
The Thermo Scientific™ EASY-nLC 1000 delivers sharper peaks for better resolution and increased protein coverage with accurate and precise solvent flow management. Dual flow sensors placed ahead of the mixer ensure precise gradients for reproducible results. nanoViper technology and a large touch screen make the system easy to set up and use. The result is more, higher quality data in less time with a lot less effort. 
Ion trap MS/MS : Thermo LTQ-VELOS with nHPLC
The Thermo Scientific LTQ Velos is evolution in the award winning LTQ family of linear ion trap mass spectrometers. Building on a tradition of innovation, the LTQ Velos™ provides the analyst with significantly enhanced performance for complex sample analyses. The innovative dual-pressure ion trap and S-Lens ion optics combine to deliver increased ion transmission along with better trapping and fragmentation efficiency. The result is the fastest and most sensitive ion trap for all applications. Continuing a commitment to providing researchers with the latest in high-performance mass spectrometers, the LTQ Velos is fully upgradeable with electron transfer dissociation (ETD) and Orbitrap™  echnology to extend its capabilities even further.
EASY-nLC II : nHPLC (Thermo Scientific)
The Thermo Scientific EASY-nLC II has been specially designed to boost the productivity of proteomic laboratories. This nano-LC instrument offers an effortless split-free nanoflow pumping system with unrivaled ease of use. The simple touch screen interface has automatic pre-configured system tests and can easily synchronize with any MS. This compact instrument provides maximum performance with 2D-enabled operation allowing the identification of more proteins compared to conventional approaches. The system provides the ultimate technology in easy maintenance, access, and service.
HT target validation through MRM-based quantitative proteomics
iFunnel Triple Quadrupole MS/MS : Agilent 6490 QQQ
The Agilent 6490 Triple Quadrupole LC/MS System incorporates iFunnel technology to give new levels of sensitivity for the most challenging quantitative analyses in pharmaceutical, clinical, food safety, and environmental applications. The quantitative power of the 6490 Triple Quadrupole is enhanced by an extended linear dynamic range. The 6490 triple quadrupole has a compact benchtop design, achieved through use of a curved collision cell. The newly designed cell also helps to reduce background noise, improving overall system signal-to-noise. New high frequency quadrupole electronics enable faster scan rates and allow for narrow mass window isolation.
Sample Preparation
UltiMate® 3000 Standard LC systems provide the right solution for demanding microbore, analytical, and semipreparative LC applications. System components are perfectly matched to meet requirements such as low extra-column and gradient delay volume for high separation efficiency and low gradient response times, as well as superior mixing performance. Analytical systems are UHPLC compatible with pressures up to 62 MPa (9000 psi).

- SmartFlow® technology for pulsation free flows even at high flow rates and pressures
- UltiFlow™ technology for nano/cap/micro flow rates (down to 50 nL/min)
- Superior binary high-pressure or quaternary low-pressure gradient proportioning
- Patented piston seal tightness monitoring
- Variable mixing volumes for optimal mixing performance
- High-precision sampling from multiple formats (well plates, vials)
- System Wellness and predictive performance indicators
- Biocompatible option for reliable and robust bioanalytical LC applications
Prefractionation of proteins and peptides prior to LC/MS analysis can dramatically increase the number of proteins ultimately identified. The Agilent 3100 OFFGEL Fractionator uses a novel isoelectric focusing technique to achieve excellent pI-based fractionation with high reproducibility. The resulting fractions are in solution, making recovery for LC/MS analysis much easier than with traditional gels.
CentriVap Benchtop Vacuum Concentrators are designed to rapidly concentrate multiple small samples using centrifugal force, vacuum and heat. As many as 132 samples may be processed at once. Sample sizes range from a few microliters up to 25 milliliters
Integrated data analysis
SORCERER™ is a fully integrated data analysis system that is compact enough to fit under a desk, yet powerful enough to run the most rigorous algorithms needed for successful pathway proteomic studies. Sensitive and comprehensive searches with multiple PTMs enabled become routine, even for large datasets. Results analysis is available with Scaffold or the Trans-Proteomics Pipeline.  SORCERER™ increases your productivity with: thousands of spectra per hour throughput; the increased accuracy from multiple algorithms; and comprehensive support through our Total Support Program (TSP). SORCERER™ 2 makes proteomics data analysis quick and easy with automated raw file searching and patented indexing acceleration of searches.
Proteome Discoverer software Identify and quantify proteins in complex biological samples using Thermo Scientific™ Proteome Discoverer™ software. Supports multiple dissociation techniques, quantitation technologies, and database search algorithms for comprehensive protein identification, characterization, and quantitation. Provides a choice of search algorithms (SEQUEST, Z-Core, Mascot, etc.) and can combine output from multiple algorithms to maximize and cross-validate results. Supports multiple dissociation techniques (CID, HCD, and ETD) for more complete coverage and confident identification of PTMs. Supports isobaric mass tagging (TMT, iTRAQ) and heavy-peptide techniques, enabling relative or absolute quantitation. Leverages high-mass-accuracy MALDI data in a Mascot-based peptide mass fingerprinting workflow. Validates protein IDs with false discovery rate (FDR) determination
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. MaxQuant is freely available and can be downloaded from this site.
The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. The Trans-Proteomic Pipeline (TPP) is a suite of software tools for the analysis of tandem mass spectrometry datasets. The tools encompass most of the steps in a proteomic data analysis workflow in a single, integrated software system. Specifically, the TPP supports all steps from spectrometer output file conversion to protein-level statistical validation, including quantification by
stable isotope ratios. We describe here the full workflow of the TPP and the tools therein, along with an example on a sample dataset, demonstrating that the set up and use of the tools is straightforward and well supported and does not require specialized informatics resources or knowledge.
Visualize and validate complex MS/MS proteomics experiments. Compare samples to identify biological relevance. Identify regulated isoforms and protein PTMs. Drill down into spectrum details and counts. Identify proteins intuitively and confidently. Create comprehensive lists of target proteins. Classify proteins by molecular function or organelle. Harness high through-put batch processing.