A recent article in the ‘Accelerating Proteomics’ blog, sponsored by Thermo Fisher Scientific, discussed the usefulness of MS-Viewer in Protein Prospector for filtering and viewing results from a wide variety of outputs, including Proteome Discoverer.
In May 2015 NSF hosted a workshop ‘Mass Spectrometry: Data to Knowledge’, where just under forty leading researchers in the proteomic community discussed current needed areas of development in computational proteomics, ranging from improvements in data acquisition, through software for data analysis, to integrating results with other data types and infrastructure that will facilitate translation into knowledge.
The final report has just been published:
Mass Spectrometry Informatics: Big Data to Knowledge
Our phosphopeptide enrichment protocol using Titanium dioxide (Titansphere) now available on the site here.
The journal Molecular and Cellular Proteomics have been a driving force behind improving and maintaining publishing standards in proteomic research. In an Editorial co-authored by three members of the Facility, along with Steve Carr from the Broad Institute, the journal has just announced updates to its publishing guidelines.
Two changes of note have been introduced. The first is a requirement for a paragraph formally describing experimental design, to make it easier to assess whether appropriate numbers and types of replicates were assayed to allow drawing of biological conclusions (of increasing importance as more quantitative studies are published). The second is the re-introduction of the requirement to submit associated raw data files with manuscript.
These guidelines will go into effect July 1st. The new guidelines can be viewed here.
The lectin wheat germ agglutinin (WGA) has affinity for terminal N-acetylglucosamine (GlcNAc) and sialic acid residues. It has four binding sites, so can bind with high affinity to branched glycan structures with multiple terminal GlcNAc moieties. However, the affinity for a single GlcNAc residue, as encountered with the regulatory modification of O-GlcNAcylation, found on serines and threonines of nuclear and cytoplasmic proteins, is low. Hence, our Resource has developed and employs a protocol where WGA attached to POROS is used as a weak affinity column to enrich for O-GlcNAc-modified peptides. You can find the protocol here:
Welcome to At the source, the blog focusing on biomedical proteomics research portfolio at the UCSF/NIH mass spectrometry national research Resource. Our portfolio of activities also includes both the discovery and targeted proteomics research efforts of the Adelson Medical Research Foundation (AMRF) consortium involved in human neuronal regeneration and repair.
We’ll be posting on research progress, technological innovation, new software tools, conferences, workshops and publications. In cooperation with MCP we will link tutorials and related instructional material that help foster development of the whole field.
Initially we will describe our current collaborative portfolio that illustrates a number of ways that chromatography, mass spectrometry and bioinformatics can be employed effectively to reveal new insights into problems at the forefront of biomedical research. Results from most projects provide unanticipated mechanistic grasps on the molecular details of cell function or dysfunction and help decipher a more sophisticated knowledge of mammalian and human biology at the protein level.
In addition, I would like to announce the launch of our newly updated website msf.ucsf.edu, and we hope you will find our blog interesting and informative. Comments are welcome.