BRIMS Center Seminars

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BRIMS Center Seminars 2016-11-10T20:10:09+00:00

Seminar presentations that explore aspects of BRIMS Center translational proteomics workflows.

Workflows for translational proteomics: crystal libraries in Proteome Discover software version 1.4. (presentation with audio, FLV)

This presentation describes the benefits of spectral libraries as well as how to build and manage Crystal spectral libraries using Thermo Scientific™ Proteome Discoverer™ software version 1.4. It also shows how Crystal spectral libraries can be used in combination with Thermo Scientific™ Pinpoint™ software to enhance translational proteomics workflows. August 17, 2014.

Crystal: a new Thermo Scientific™ Proteome Discoverer™ software node for building high-quality spectral libraries. (PDF 3.4 MB)

Using mass spectral libraries to interpret unknown mass spectra is not new. However, because of the rapid growth in publicly available proteomics data, spectral searching is now an alternative to sequence-based database searching.

Spectral searching is typically faster than sequence-based searching because it searches a much smaller data set. Spectral searching also takes full advantage of the richness of all mass spectral features, including actual peak intensities, neutral losses, and uncommon fragments, to determine the best match. Therefore scoring of matches is generally more precise and better at discriminating between good and bad matches.

This presentation reviews the ways that Crystal spectrum libraries can improve proteomics assays and speed up SRM assay development.


Changing the way you ask questions about your biological system (webinar)

This presentation describes new experiments for deep proteome sequencing, multiplexing, structure elucidation and identification of low-abundance proteins with extreme throughput, sensitivity and quantitative accuracy. July 25, 2013.

Routine quantitation of peptide-based therapeutics on the Q Exactive Mass Spectrometer: Qual/quan method development for endogenous and therapeutic analogs (presentation with audio, FLV).

This presentation discusses the challenges of peptide-based quantitation. An automated targeted workflow for the analysis of insulin variants is presented. Qual/Quan strategies using for data extraction, verification, and quantification using Pinpoint software are discussed. June 13, 2013.

A translational proteomics workflow coupling immunoenrichment to selected-reaction monitoring (MSIA-SRM) and its application to alzheimer’s disease.

One of the biggest challenges in the translation of mass spectrometry (MS)-based biomarkers into the development of clinical research methods is the lack of fully developed tools and workflows to deliver the throughput specificity, sensitivity, and robustness needed for clinical applications. In addition, many existing protein biomarker candidates may prove too non-specific to be clinically useful such that significant discovery work focused on protein isoforms still remains to be done. December 10, 2013.

Proteomics delivers on its promise: using innovative mass spectrometry to pave the way for multi-protein biomarker verification

The primary goal of this presentation is to highlight a workflow for the integration of unbiased biomarker discovery with hypothesis-driven, targeted assay development in a seamless manner. Mass spectrometry has typically been the technology of choice in the search for proteomic biomarkers, but the translation of this information into high-throughput assays that facilitate the verification of putative markers has not been straightforward.

SRM-based assays provide a powerful vehicle for the verification and implementation of putative biomarker information derived from high-resolution LC-MS/MS experiments because of their selectivity, sensitivity, robustness and speed.

In this report, we describe the development and application of bioinformatics algorithms, including a novel application of ROC curves allowing efficient mining of LC-MS/MS discovery data with subsequent integration into SRM methods, thus paving the way for future biomarker verification with larger clinical cohorts. June 15, 2010.


Other Presentations

To achieve its mission, the BRIMS Center collaborates with leading researchers and its parent organization, Thermo Fisher Scientific. These presentations document this work.

Development of Multiplexed Mass Spectrometric Immunoassay (MSIA)-SRM methods for proteins associated with alzheimer’s disease and application to clinical samples for research only (PDF 3.7 MB)
This presentation describes the development of novel multiplexed mass spectrometric immunoassay (MSIA) selected reaction monitoring (SRM) methods for the detection and quantification of Aβ and Apo E peptides in human cerebrospinal fluid and plasma.

Crystal: a new PD node for building high quality spectral libraries (PDF 3.39 MB)
BRIMS PD Users Meeting, October 23, 2013

Serendipity in the blood: Mass spectrometry in the discovery of clinical biomarkers (PDF 713 KB)
AFMR Symposium, Boston, 4/24/13 Mary F Lopez, Director BRIMS Biomarker Research Initiatives in Mass Spectrometry

California wine LC/MS analysis with SIEVE 2.0. (PDF 2.76 MB)
Michael Athanas, Ph.D. VAST SCIENTIFIC / BRIMS; Mark Dreyer, Ph.D. Thermo Fisher Scientific

Identification and quantification of in vitro peptide metabolites using a novel mass spectrometry-based workflow (PDF 2.77 MB)

Regular or decaf? Options for quantitative biomarker discovery (PDF 2.58 MB)
Conference Mass Spectrometry Applications in Clincal Laboratories, San Diego, Feb 2011

Novel MS discovery-to-targeted SRM workflows incorporating ROC curve analysis of putative biomarker candidates in bona fide clinical samples (PDF 3.41 MB)
Sweedish Proteomics Society, Gothenberg, Sweden, Nov 2010

Targeted SRM assays: creating a new clinical paradigm (PDF 1.9 MB)
AACC Conference. Washington D.C. 7/30/08