Lab Expectations

If the thought of self-cannibalization is not appealing to you, you may not want to read the next sentence . . . Your cells are literally eating themselves right now! In the 1960s, Christian de Duve named this process “autophagy” from the Greek auto (self) and phagein (to eat). He was later awarded the Nobel Prize for Physiology or Medicine for his contribution to the cell biology field. Little did de Duve know what an issue this word would cause: do you pronounce it “aw-tof-a-gee” or, “auto-fay-gee”? Well, actually – it’s a bit like tom-ay-tow/tom-ah-tow – both are right! As de Duve himself said, “I coined the word, but not the pronunciation.”

Boston is famous for the Red Sox, baked beans, and for having a distinctive accent. What you may not know is that it’s also renowned for its thriving scientific community. With hundreds of colleges, biotech, and pharmaceutical companies in the Greater Boston area, what better location for Seeding Labs a non-profit organization whose mission is to help talented scientists in developing countries to conduct life-changing research. With help from the community they provide these scientists with the resources they need but might not have access to, including lab equipment, training, and access to key influencers in their field.

BioPlex: a protein interaction network created from thousands of protein immunopurifications

Steven Gygi, Ph.D
Professor in the Department of Cell Biology, Harvard Medical School

Protein-protein interactions form a network whose structure drives cellular function and whose organization informs all biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains...

Part 1 gave an overview on mass spectrometry-based proteomics. Now it’s time to talk about how this strategy can be used to identify peptides with post-translational modifications (PTM) from a complex biological sample.

Thinking about lab expenses isn’t as enjoyable as investigating your favorite signaling pathway. However, because research money is hard to come by, it is something that should be considered when picking your reagents for western blotting. It makes sense to keep the quality of your primary antibody in mind, because the success of the entire experiment depends on the antibody being reliable, specific, and sensitive. If the antibody does not perform as expected your experiment may fail . . . and the cost of a failed western blot may be more than you think.

After sequencing of the human genome was complete, it was time to roll up our sleeves and get started on the daunting task of unraveling the complexity of the proteome. Thus the era of proteomics, the study of the function of all expressed proteins, was born. This task is especially complicated

Boston is famous for the Red Sox, baked beans, and for having a distinctive accent. What you may not know is that it’s also renowned for its thriving scientific community. With hundreds of colleges, biotech, and pharmaceutical companies in the Greater Boston area, what better location for Seeding Labs a non-profit organization whose mission is to help talented scientists in developing countries to conduct life-changing research. With help from the community they provide these scientists with the resources they need but might not have access to, including lab equipment, training, and access to key influencers in their field.

BioPlex: a protein interaction network created from thousands of protein immunopurifications

Steven Gygi, Ph.D
Professor in the Department of Cell Biology, Harvard Medical School

Protein-protein interactions form a network whose structure drives cellular function and whose organization informs all biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains...

Post Translational Modification: Antibody Enrichment for Mass Spectrometry-based Proteomics

Continuing our theme of simplifying proteomics we present a webinar featuring Matthew Stokes, Ph.D., principal scientist of the proteomics group here at Cell Signaling Technology and Christopher Rose, Ph.D., a postdoctoral research fellow in the Gygi Lab at Harvard Medical School.

Dr. Stokes describes PTMScan^® technology, a method that uses antibodies to enrich specific post-translationally modified (PTM) peptides (e.g., phosphorylated, methylated, ubiquitinated etc) from a complex mixture prior to LC-MS/MS analysis. Dr. Rose demonstrates how, by combining PTMScan technology with isobaric labeling, specifically with tandem mass tags (TMTs), his lab quantified over 15,000 ubiquitination events in Bortezomib treated cells.

Part 1 and part 2 introduced mass spectrometry-based proteomic methods, like PTMScan^®, for the study of post-translational modifications (PTMs). In the final part of this series you can see how PTMScan can be applied in translational research.