Our Facilities


Lighthouse Proteomics is located in Beverly, Massachusetts at the Cummings Center in a newly renovated area of a historic facility once known as the United Shoe Machinery Corporation, one of the largest and oldest industrial sites in the United States. The laboratories are equipped with state-of-the-art analytical instrumentation, sample preparation tools and data analysis software to address a wide range of proteomic applications.

Lighthouse Proteomics is located in Beverly, Massachusetts at the Cummings Center in a newly renovated area of a historic facility once known as the United Shoe Machinery Corporation, one of the largest and oldest industrial sites in the United States. The laboratories are equipped with state-of-the-art analytical instrumentation, sample preparation tools and data analysis software to address a wide range of proteomic applications.

Lighthouse Proteomics uses the ThermoFisher Q Exactive is a hybrid quadrupole-Orbitrap mass spectrometer combining the high-performance quadrupole mass filter with the industry leading high resolution sensitive and selective Orbitrap mass analyzer.

Lighthouse Proteomics uses the ThermoFisher Q Exactive is a hybrid quadrupole-Orbitrap mass spectrometer combining the high-performance quadrupole mass filter with the industry leading high resolution sensitive and selective Orbitrap mass analyzer.

The facilities also include a Bruker Autoflex Speed MALDI-TOF/TOF for reliable and detailed protein/peptide characterization we well as cutting edge applications for high resolution imaging & array analysis.

The facilities also include a Bruker Autoflex Speed MALDI-TOF/TOF for reliable and detailed protein/peptide characterization we well as cutting edge applications for high resolution imaging & array analysis.

The Bio-Rad V3 Western Workflow™ with ChemiDoc™ Touch imaging is used at Lighthouse Proteomics to perform western screen studies to help optimize experimental conditions (treatment conditions, time points, compound choice or dose, cell line or tissue choice) for proteomic experiments. The screening method is used to identify responsive post-translational modifications and the corresponding PTM antibody reagents for subsequent immunoaffinity LC-MS/MS studies.

The Bio-Rad V3 Western Workflow™ with ChemiDoc™ Touch imaging is used at Lighthouse Proteomics to perform western screen studies to help optimize experimental conditions (treatment conditions, time points, compound choice or dose, cell line or tissue choice) for proteomic experiments. The screening method is used to identify responsive post-translational modifications and the corresponding PTM antibody reagents for subsequent immunoaffinity LC-MS/MS studies.

The SageELF electrophoresis system from Sage Science is used to conduct automated molecular weight fractionation of protein samples using pulse-field electrophoresis to reduce complexity for subsequent LC-MS/MS analysis.

The SageELF electrophoresis system from Sage Science is used to conduct automated molecular weight fractionation of protein samples using pulse-field electrophoresis to reduce complexity for subsequent LC-MS/MS analysis.


Lighthouse Proteomics uses the Comet-SEQUEST® database search engine to identify proteins from primary sequence databases and is the newly developed descendent of the original SEQUEST® search engine released in 1994 (Eng JK, Jahan TA, Hoopmann MR (2013) Comet: An open-source MS/MS sequence database research tool. Proteomics, 13(1) 22-24).

Lighthouse Proteomics uses the Progenesis QI data processing software for quantification of peptides and proteins. Progenesis QI is developed and distributed by Nonlinear Dynamics (Waters Corp) and is recognized for its capabilities for its accuracy and efficiency as a proteomics discovery analysis tool for both MS/MS and MS based applications. In addition, we also use Skyline and XcaliburTM (Thermo Scientific) software for our quantitative proteomic applications.


Lighthouse Proteomics would like to acknowledge the Massachusetts Life Sciences Center and the Life Sciences Consortium of the North Shore as well as North Shore InnoVentures for their support.

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