Proteomics (La Jolla)

Overview

The Sanford-Burnham Proteomics Facility provides state-of-the-art mass spectrometry-based proteomics services with methods tailored to the needs of scientific investigators for routine mass spectrometric analysis of peptides and proteins, identification of novel proteins, characterization of post-translational modifications, and quantitative proteomics analysis of simple to complex biological samples. The facility identifies, validates and develops new methods designed for the characterization and identification of biologically important proteins. It also supports users with software applications and development, data analysis and experimental design of proteomics studies. The facility is continuously expanding its capabilities in large-scale differential proteomics analysis and phosphoproteomics for unbiased discovery of potential biomarkers and mapping protein profiles. We provide proteomics services to Sanford-Burnham scientists as well as outside non-profit and for-profits organization on a fee-for-service basis.
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Services

  • Molecular weight determination of proteins, peptides, oligonucleotides, glycans and polymers
  • Protein identification from gel or solution using 1D LTQ LC/MS/MS or MALDI TOF TOF Mass Spectrometry
  • In-gel or in-solution digestion and proteomics sample preparation
  • 2D and 3D LC/MS/MS analysis by multi-dimensional liquid chromatography separations coupled directly to Michrom low-flow ESI-OrbiTrap XL and Velos Pro
  • Protein identification for large scale proteome analysis of mid to complex samples
  • 2D gel electrophoresis for protein separation
  • Differential Proteomics Analysis using Mass Tagged (iTRAQ,SILAC,15N/14N/TMT) and label-free differential LC/MS/MS data analysis
  • PTM mapping to identify post-translational modifications such as phosphorylation, ubiquitination or other PTMs
  • LC/MS/MS Database search, Peptide tandem mass spec sequencing and Peptide mass mapping by comparison to a theoretical in-silico-digest
  • Training on MALDI TOF and TOF TOF: 1 day training course with two-week hands on training with follow-up offered by members of the facility necessary for hourly usage of the Bruker Autoflex II MALDI TOT TOF instrument
  • Protein Quantification using AQUA Technology

Equipment and Resources

  • Thermo LTQ OrbiTrap Velos Pro with ETD mass spectrometer (Phosphoproteomics/PTM analysis for Mid to complex)
  • Thermo LTQ OrbiTrap XL Hybrid mass spectrometer (protein ID/PTM analysis for Mid to complex samples)
  • Thermo LTQ linear ion trap mass spectrometer used (protein ID/PTM analysis for gel slices and IP samples)
  • MALDI TOF/TOF Mass Spectrometer (Bruker Daltronics AutoflexII for MW determination analysis)
  • HCT Ultra Mass Spectrometer (Bruker Daltronics) and Proteineer liquid handler
  • Ettan DALT six large vertical system and Ettan IPGphor IEF system for 2D gel Electrophoresis Analysis
  • Automated spot handler (Shimadzu Biotech Xcise)

Price List


1D and 2D gel with Coomassie or Sypro stainGel150187.5202.5394.5K600
1D LC/MS/MS protein identification (10-14 Days)Sample150187.5202.5394.5K981
1D LC/MS/MS protein identification (7 Days)Sample5006256751315K985
2D gel with silver stainGel250312.5337.5657.5K610
2D LC/MS/MS protein identification complex sampleSample800100010802104K986
2DE sample cleaningSample202527.552.6K105
3D LC/MS/MS protein identification with PTM for complex samples:PhosphoproteomicsSample2000250027005260K999
Analysis Level 2 (10-100 proteins expected)Each1000125013502630K125
Analysis Level 3 (100+ proteins expected)Each2000250027005260K126
Consultation, hourlyHour5062.567.5131.5K900
Data analysis hourlyHour5062.567.5131.5K910
Differential LC/MS/MS Analysis: IP2/Census,QTools for label-free data analysis and IP2/Census for SILAC, iTRAQ, N14/N15 and TMT data analysisEach200250270526K124
DIGE: Fluorescent labeling and imaging, 2 Dye (Cy3,Cy5)Sample250312.5337.5657.5K104
ESI-MSSample5062.567.5131.5K140
HPLC hourlyHour7593.75101.25197.25K300
IEF serviceStrip2531.2533.7565.75K106
In-Gel digestion only (no ID)Sample5062.567.5131.5K171
In-Solution digestion (no ID)Sample7593.75101.25197.25K172
MALDI-MS ourly usageMin7593.75101.25197.25K130
MALDI-TOF Hands-on trainingEach300375405789K120
MALDI-TOF MW DeterminationSample5062.567.5131.5K100
Mass Spectrometry sample special treatment (e.g. Ziptip C4,C18)Sample1518.7520.2539.45K121
Miscellaneous chargesEach111.352.63K983
Peptide mass mapping - MALDISample150187.5202.5394.5K170
PTM Analysis from low complex sampleSample4005005401052K984
Special sample handlingHour5062.567.5131.5K110
Spot picking serviceGel607582.5157.8K107
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