PCF SERVICES AND PRICING INFORMATION- April 2013
The University of British Columbia Proteomics Core Facility (PCF) is part of the Center for High Throughput Biology
(CHiBi), and The Michael Smith Laboratories (MSL). We gladly accept samples from UBC and other academic Institutions
(ACAD), Canadian Non-profit (CNP) and Corporate (COR) researchers worldwide. We offer a variety of techniques and
services to help in you research. Use this guide in conjunction with personalized advice to get the most efficient use of
our services. All prices listed are per sample, unless otherwise noted.
The CHiBi Proteomics Core Facility has offered Mass Spectrometry and analytical services since 2002, and has not
raised our prices since then. Due to the rising costs of labour, machinery and reagents, it is necessary to change our
prices to cover these rising costs. A ~10% increase in the cost of our services will come into effect on April 1, 2013
which is reflected in the prices below.
Ultimately, prices and workflow are a collaborative process between the client and PCF manager, Suzanne Perry.
Please email Ms. Perry to discuss your project and together a quote can be generated.
Sample Cleanup
Stage Tip or Drop Dialysis
Detergent Removal via column (per sample)
SDS-PAGE
ACAD
CNP
COR
$9
$15
$82
$15
$20
$110
$20
$28
$150
Mass Spectrometry is a very sensitive technology for analyzing protein, peptide, and other organic molecules. However,
this means that contamination will affect the data you get. Samples that contain excessive keratin, incompatible buffers
(see our web page for more details), high concentrations of salts, etc., will negatively impact analysis, from depressing
the signal detected, to masking components present, to clogging the Mass Spectrometer. Therefore, it is imperative that
we do all we can to protect your sample, and the machines.
Sample Preparation
ACAD
CNP
COR
Tryptic Digestion (1-10 samples)
Tryptic Digestion (10-30 samples)
$215
$275
$275
$330
$330
$400
Phosphopeptide enrichment (TiO2 tips or ZrO2 tips)
Reductive Dimethylation with formaldehyde for quantitation
BCA/Bradford protein Assay
Densitometry of SDSPAGE for Protein Quantitation+Report
Quantitation Report
$30
$85
$66
$70
$55
$40
$150
$75
$85
$90
$55
$175
$95
$100
$125
Depending on your research needs, and what information you hope to get out of your sample(s), there are preparations,
and manipulations required prior to Mass Spectrometric analysis. Consult the PCF staff for any questions you may have
on these techniques.
MALDI-TOF Mass Analysis
ACAD
CNP
COR
Mass Determination
Long Term Client (LTC) Training/per hour *(4 hours minimum)
Hourly rates for trained LTC
$55
$132
$75
$85
$330
$110
$125
$550
$165
The PCF uses an Applied Biosystems Voyager DESTR with a mass accuracy from 0.001-0.05%, with accurate mass
determination of proteins and peptides from <1000 to 300,000Da. Can be run in positive, or negative ion mode; linear,
or reflectron mode. Can be used to analyse samples of lipids, synthetic polymers, carbohydrates, glycoproteins, RNA,
DNA/ oligonucleotides, and organic molecules; C-terminal amino acid sequence determination by Carboxypeptidase Y
(CPY) digestion and MALDI-TOF MS. Post Source Decay (PSD) sequencing available for peptides <2500 Da. After training
by PCF staff, LTC clients can book time on the MALDI-TOF to conduct their own analysis at an hourly rate.
Electrospray Mass Analysis- API Q-STAR XL LC Packings
Ultimate HPLC
ACAD
CNP
COR
LC-MS: intact mass analysis or Post Translational Modification
(PTM) detection
LC-MS/MS analysis, MASCOT database search and report
$140
$165
$190
$250
$300
$330
De novo sequencing for PTM confirmation of previously
detected PTM in LC-MS
$195
$250
$330
Electrospray Mass spectrometry is performed on an API Q-STAR PULSARi Hybrid LCMS/MS equipped with both an
IonsprayTM and a Protana Nanospray front-end. The Flow rates from 2 nl to 200 μl per minute with sensitivity down to
femtomolar level. Dionex FAMOS suite of liquid chromatography units are coupled to the Q-STAR to provide
unparalleled performance in LCMS/MS applications.
Q-Star Analyses can provide:
♦ Peptide Mass Fingerprinting
♦ Automated de novo peptide sequencing
♦ in silico proteolytic digest generation
♦ Compatibility with MASCOT on-line search software
♦ Post translational Modification (PTM) detection and confirmation: Phosphorylation, Sulfation, Ubiquination,
Glycosylation, etc…
PLEASE NOTE: LC runs that exceed normal times will incur additional charges of $100.00/hour, in 30 minute increments.
LTQ-Orbitrap VELOS
Orbitrap analysis, raw file conversion, MASCOT database
search and report
ACAD
CNP
COR
$275
$360
$560
The LTQ-Orbitrap fragments its samples with the usage of Collision Induced Disassociation (CID), as well as Higher
energy Collision induced Disassociation (HCD) It also contains a Curved Linear Trap (CLT) that allows the ions to
accumulate which boosts the ion signals. A higher sensitivity can be achieved with this and therefore, samples can
realize ideal results on the Orbitrap. Currently the LTQ Orbitrap is used for highly complex proteomic samples, such as
sub-cellular whole lysates, or immune-precipitation /pull down and protein-protein experiments.
Peptide Synthesis- 5-10 micromolar scale- this service is exclusively for MRM workflows within the PCF: Please consult
with PCF staff for pricing.
Off-Gel Isoelectric Focusing- OFFGEL electrophoresis is a novel technique jointly developed by Agilent Technologies and
Diagnoswiss that separates proteins or peptides according to their isoelectric points, whereby the separated
components are recovered in liquid phase. Up- or downstream sample processing steps such as immunodepletion,
protein digestion and liquid chromatography can be easily interfaced with this technique for multi-dimensional
separations of complex samples.
ACAD/NPR/COR
Fractionation variable
** Pricing will depend on the amount of samples and hours you spend on the equipment. Please refer to the staff for
your pricing needs. **
SAMPLE WORKFLOW FOR PROTEIN IDENTIFICATION FROM SDS-PAGE GEL SUBMISSION
In-Gel Tryptic Digestion  Q-STAR LC-MS/MS or Orbitrap Velos LC-MS/MS MASCOT database search
SAMPLE WORKFLOW FOR IDENTIFICATION FROM AN IP
SDS-PAGE sample cleanup  In-gel Tryptic digestion Orbitrap Velos LC-MS/MS MASCOT database search
Quantitation with Proteome Discoverer
SAMPLE WORKFLOW FOR RELATIVE QUANTITATION (WITH PROTEOMICE DISCOVERER)
SDS-PAGE sample cleanup  In-Gel Tryptic digestion  Reductive dimethylation with formaldehyde labeling  Stagetip cleanup and concentration  Orbitrap Velos LC-MS/MS  MASCOT Database search  Quantitation with Proteome
Discoverer
More complex analysis, for example, multiple experimental time points, from multiple SILAC labeled samples will require
not only the analysis mentioned above, but fractionation by off line HPLC (HILIC, size exclusion, SCX or C4,8 or 18). Each
fraction then requires an individual LC-MS/MS run, so please consult with PCF staff to plan an appropriate course of
action. Below is one representative schematic of a quantitative workflow with a complex sample.
Ver April 2013