VA Palo Alto and Stanford DDC Mass Spectrometry Core (operated by the Robinson Laboratory)

Download Mass Spectrometry Guidelines and Information Form (Word .doc format)

The Palo Alto VA and Stanford DDC Mass Spec Facility has an Agilent XCT Plus ion trap mass spectrometer equipped with a 1100 series liquid chromatrography unit, nanoflow pump, and orthogonal nanospray source. The machine also has an optional MALDI source. The nanospay is generally recommended for protein identification, while the MALDI source is recommend for confirmation of synthesized peptides (size determination).

Types of analysis available:

1. Protein identification
2. Peptide quality control (confirming size using MALDI)
3. Analysis of post-translational modifications

What the user needs to do:

1. Provide the Core with trypsin digested sample(s):

(i) from a gel band/spot using the Pierce In-Gel Tryptic Digestion Kit(Pierce cat # 89871, 150 digestions, $191) (no further clean-up necessary)


(ii) from solution using the Pierce In-Solution Tryptic Digestion andGuanidination Kit (Pierce cat # 89895, $300), and perform further sample clean-up with Pierce PepClean C-18 Spin Columns (Pierce cat # 89870, 25 columns, $65). For clean up users will also need: Trifluoroacetic acid (Sigma cat# 74564-1ML-F ; price $17) and Acetonirile (Fisher cat#A9981, price $25.30).

  • for all of these protocols researchers must use HPLC-grade water (Fisher, cat #W5-1, 1L, $60)
  • for more than 10 samples, users are asked to provide samples in 96-well plate (Agilent, Cat # 5042-1386, $21.7) sealed with a closing matt (Fisher, cat # 276011, 50 mats, $243.93)

2. Complete the below form and bring your samples to Building 100, D3-111.

3. Analyze the resulting .mgf data file with Mascot Software (Matrix Science; to identify the proteins and/or modifications present

What the Core does:

1. Run your sample(s) on the mass spectrometer
2. Provide you with your data:

  • Email you your .mgf files
  • upon request provide a CD/DVD containing the raw data

3. Provide technical advice regarding sample preparation, processing and data analysis
4. Provide assistance for preparation of up to 10 samples per lab per year

Facility Contact Info:
Orr Sharpe, PAVAHCS Building 100, D3-111, (650) 849-0148