Protein Identification
A peptide centric (bottom up) approach using nanoLC-MS/MS and multiple modes of fragmentation (CID, HCD, ECD) to identify the amino acid sequences of peptides.
Vincent Coates Foundation
COVID-19 status: SUMS is safely supporting research under current physical distancing and occupancy rules. Meetings and seminars continue to be held via Zoom. Email us at spectrometry@stanford.edu. More info
SUMS Weekly Office Hours
Have a question about a potential mass spec project?
Not sure exactly who to talk with at SUMS?
Drop in to our open virtual office on Tuesday afternoons between 4:15 and 4:45 pm Pacific Time and get answers!
Not sure exactly who to talk with at SUMS?
Drop in to our open virtual office on Tuesday afternoons between 4:15 and 4:45 pm Pacific Time and get answers!
Zoom link: https://stanford.zoom.us/j/98694419513?pwd=WUpQcVlsbXFxYkRUQUp6WE1Db080QT09
Password: 009760
Password: 009760
Proteomics
Post Translational Modification (PTMs)
Identify and localize PTMs such as phosphorylation, acetylation and oxidation with and without enrichment strategies.
Protein Differential/Expression Analysis
Relative Qualitative and Quantitative approaches indicating protein levels within the same sample as well as differential levels among samples. A variety of approaches exist within this category -- please read further.
Peptide Mapping/Complete Protein Characterization
Non-de novo approach, analyzing peptides of a protein of a highly pure source (including basic modifications). Multiple proteases to provide overlapping sequence information as well as alignment are often necessary. Intact analysis of the pure proteoform(s) is also complementary.
Intact Protein Characterization
Determination of the intact molecular weight of a highly pure protein.
Targeted Peptide/(MRM/SRM)
Absolute, targeted quantitative analysis of peptides using SRM approach.
Sample Preparation
Instructions on sample preperation
Publications
Architecture of an RNA Polymerase II Transcription Pre-Initiation Complex Science
Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, Levitt M, Kornberg RD
2013 Nov 8;342(6159):1238724. doi: 10.1126/science.1238724. Epub 2013 Sep 26
A Simple Method for Purification of Vestibular Hair Cells and Non-Sensory Cells, and Application for Proteomic Analysis Public Library of Science
Herget M, Scheibinger M, Guo Z, Jan TA, Adams CM, Cheng AG, Heller S.
2013 Jun 4;8(6):e66026. doi: 10.1371/journal.pone.0066026. Print 2013
Mass spectrometry compatible surfactant for optimized in-gel protein digestion Analytical Chemistry
Saveliev SV, Woodroofe CC, Sabat G, Adams CM, Klaubert D, Wood K, Urh M.
2013 Jan 15;85(2):907-14. doi: 10.1021/ac302423t. Epub 2013 Jan 7
FAQs
When can I expect to recieve my protein identification results?
Typical turnaround time for protein ID is 7-10 working days.
What protocol is used for in-gel digests?
What protocol is recommended for silver-staining and destaining polyacrylamide gels?
