The Blais Proteomics Center develops and applies state-of-the-art proteomics, informatics, and related technologies for direct interrogation of protein expression, modification, and function in response to biological perturbation in cell-based models of human cancer and primary tissues. The Blais Proteomics Center serves as a valuable resource to support individual research labs at the Dana-Farber and throughout the surrounding research community. As a key component of Dana-Farber’s Strategic Plan for Research, Blais Proteomics actively participates with other Dana-Farber Strategic Research Centers in large-scale studies, designed to leverage disparate capabilities in pursuit of novel, in-depth, and otherwise unattainable insights into human biology and disease. Consistent with our role as a world-class, center of excellence in proteomics science, members of the Blais Proteomics center contribute to the teaching mission at Harvard Medical School and participate in outreach activities designed to introduce and train young scientists and others who may not otherwise have access to these advanced technologies.
"The Mass Informatics Group at the Blais Proteomics Center creates software tools and algorithms engineered around a zero infrastructure philosophy. This means our data analytic framework is designed for installation and operation with minimal sys admin support. Our tools are well suited for in-depth, manual exploration of individual data features and are nonetheless compatible with high-throughput environments."
"We have experience with a number of multi-dimensional fractionation techniques, including SCX-RP, RP-RP, and HILIC-RP. In addition we have a very active program in development and application of immunological- and chemical-based protocols for enrichment of phosphorylated peptides and proteins. Our fractionation and enrichment techniques can be combined with stable isotope labeling to monitor the response of signaling cascades to biological perturbation. In addition, Blais Proteomics is equipped with a number of state-of-the-art mass spectrometers that support qualitative and quantitative analysis, coupled to both electrospray- and laser-based ionization and sample introduction."
"There is a growing appreciation that control of cellular processes occurs through a delicate balance of protein post-translational modification and protein interactions with other proteins, DNA, RNA, and small molecule metabolites. Hence the identification a protein’s interactions partners can provide valuable insights into its biological role, molecular function and regulation. The development of tandem affinity purification (TAP) techniques has facilitated the isolation of discrete protein complexes from physiological contexts. The use of mass spectrometry-based proteomics combined with TAP provides for rapid and sensitive detection of protein complex constituents.
We have established standard protocols spanning all aspects of protein complex analysis, from efficient sub-cellular fractionation to a user-friendly framework for data analysis. Our use of gel-free protocols in combination with stable isotope labeling enables a relative quantitative measure of protein complex dynamics in response to biological perturbation (DNA damage, signal transduction, cell death, etc.). Over the past few years, we have analyzed a wide range of target proteins – transcription factors, cell cycle regulators, enzymes, RNA and DNA binding proteins –purified from a variety of cell lines and model systems (s.cerevisiae, d.melanogaser, mouse tissues), using FLAG:HA and other variants of the TAP technique."
"multiplierz is an open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers' proprietary data files via mzAPI. User-defined customization, flexibility, and ease-of-use are central themes in our development efforts. Built-in multiplierz tools include:Automated download of peptide database search results. Built-in multiplierz tools include:
* Identification driven annotation of precursors
* Tools to support iTRAQ and label-free quantification
* Multiple file consolidation and manipulation
* Interactive viewer for dynamic access to spectra
* Retrieval of Genbank information
* In-silico digestion and fragmentation
multiplierz generates portable, information rich spreadsheet-based reports with images (spectra, reconstructed ion chromatograms, etc.) embedded in cell comments. The interactive "Peak Viewer" provides an environment for in-depth interrogation of data, image editing and exporting, and comparison of multiple spectra."
"The goal of the mzAPI project is to define, develop and promote a common application programming interface as a universal mechanism for proteomics data access and analysis. This new strategy will allow researchers to share and query native files, whether or not they generated the data, or even own a mass spectrometer. Towards this end we have developed a very simple API (mzAPI) in Python, with the intention that it be equally accessible to programmers and non-programmers alike.
The 5 basic function calls available through mzAPI are:
scan(time) --> [(mz,intensity)]
scan_list(start_time,stop_time) --> [(time,precursor)]
time_range( ) --> (start_time,stop_time)
scan_time_from_scan_name (scan_name) --> time
ric(start_time,stop_time,start_mz,stop_mz) --> [(time, intensity)]"
"Pathway Palette is a rich web-based application that enables researchers to view their proteomics data in the context of pathways and networks. Significantly, all underlying peptide- and quantification-level data are retained and available for query by the user. Pathway Palette accepts peptide sequences as input, either via copy-and-paste or through upload of multiplierz formatted spreadsheets."