PUBLICATION QUESTIONS:
I am writing a paper that includes data acquired at SUMS -- what should I put in the experimental?
Please feel free to contact us regarding experimental writeups. We will be glad to help you with the content and/or review the text.
I am writing a paper that includes data acquired at SUMS -- how should the lab be acknowledged?
The lab should be referred to as "the Vincent Coates Foundation Mass Spectrometry Laboratory, Stanford University Mass Spectrometry (http://mass-spec.stanford.edu)". Acknowledgements of individuals when appropriate for outstanding assistance are always appreciated as well. Please send us the title and reference of the paper when it is published; this information is needed for our records. You can also request to have the paper listed on our publications page.
NIH requirement for Orbi data: Each publication, press release or other document that uses data from the LTQ-Orbitrap Velos instrument must include an acknowledgement of NIH grant support and disclaimer such as the following: "The project described was supported by Award Number S10RR027425 from the National Center For Research Resources. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Center For Research Resources or the National Institutes of Health."
PROTEOMICS QUESTIONS:
When can I expect to recieve my protein identification results?
Typical turnaround time for protein ID is 5-8 working days.
What is MudPIT, and what can I expect from a MudPIT analysis?
MudPIT is an acronym for "Multidimensional Protein Identification Technology" originally developed in the lab of John Yates at Scripps. (see "Large-scale analysis of the yeast proteome by multidimensional protein identification technology." MP Washburn, D Wolters, JR Yates 3rd, Nature Biotechnology 2001, 19(3), 242-7. abstract). After enzymatic digestion of a protein mixture, the peptides are separated chromatographically. The two dimensions of separation consist of strong cation exchange (SCX) chromatography, followed by reverse phase (RP) chromatography. Peptides eluting from the RP separation are analyzed by ESI-MS/MS. MudPIT is a powerful technique for analyzing complex protein samples, from immunoprecipitations to organelle preps to whole proteomes. Combining MudPIT with the vented column concept from Steve Gygi at Harvard (see "Automation of Nanoscale Microcapillary Liquid Chromatography-Tandem Mass Spectrometry a Vented Column." lJ Licklider, CC Thoreen, J Peng, SP Gygi. Analytical Chemistry 2002, 74, 3076-3083. abstract), SUMS has developed a high resolution variation of MudPIT using long (60 cm) vented capillary columns. Details regarding long column vented MudPIT have been published; the reference can be found on the Publications page (see featured paper). Practical information and example MudPIT results are located on the Services page.
What protocol is used for in-gel digests?
What protocol is recommended for silver-staining and destaining polyacrylamide gels?
Our recommended silver staining and destaining protocol is taken from Gharahdaghi, et. al. Electrophoresis 1999, 20, 601-605. abstract
CHEMISTRY QUESTIONS:
I have a compound that is air/water sensitive, can it be analyzed by mass spec?
Please contact us regarding your particular compound. Arrangements can be made to analyze your sample immediately upon arrival at an agreed-upon time. We may ask you to prepare the sample solution in your drybox and bring it to the mass spec lab in special "packaging" along with a small amount of rigorously dry, degassed solvent.
