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You are hereUNIL > Center for Integrative Genomics > Protein Analysis Facility > Services and Fees

Services and Fees

IMPORTANT :

* Fees valid for samples submitted AFTER February 1st, 2017

* "Lausanne academic" includes UNIL, CHUV, EPFL, Ludwig institute

* Mass spec/protein ID : all prices are intended per sample submitted, in swiss francs (CHF)

* Gel separation : all prices are intended per gel in swiss francs (CHF)

* DISCOUNTS (not cumulative):

- 10% for more than 10 samples submitted simultaneously;

- 10% for invoices > 5'000 CHF;

- 15% for invoices > 10'000 CHF;

- 20% for invoices > 20'000 CHF.

* All prices can be subject to change without prior notice

 


Click on the description for more details on every service workflow offered
 
MASS SPECTROMETRY and PROTEIN IDENTIFICATION 
No. Description Applicability Lausanne
academic
External
academic
Private
(commercial)
1 Protein identification by short LC-MS run simple mixtures, samples from 1D gel bands or 2D gel spots [More] 100 200 300
2 Protein identification by nanoLC-MS/MS : long LC-MS run 1D gel bands for in-depth analysis; medium complexity mixtures with max sensitivity [More] 160 320 500
3 Direct protein identification by nanoLC-MS/MS medium complexity mixtures; only for samples ready to inject (requires setup tests) [More] 100 200 not done
4 Special data analysis (per hour) customized database setup, PTM quantitation, label-free quantitation, quantitation from targeted MS analyses, ... [More] 50 100 200
5 Direct electrospray analysis protein/peptide intact mass [More] 120 250 400
6 Sample preparation (desalting...) clean up before analysis (often necessary for 2,5) [More] 60 150 220
7 Large scale sample preparation, processing and QC extraction and digestion of up to 20 mg material from cells or tissues, digestion, desalting and QC [More] 650 900 1200
8 PTM identification workflow determine site(s) of modification of a protein of interest; may include a second digestion with a different protease and/or MS reanalysis with different methods (ETD) if needed; price includes PTM quantitation across samples. NOTE : more complex cases may require price supplement for special data analysis (see nr.4) [More] 300 450 700
9 Shotgun analysis of complex samples low or medium complexity mixtures: protein complexes or subcellular fractions. Gel separation workflow with 4-6 fractions [More] 700 1200 2000
10 Extended shotgun analysis of complex samples more complex samples; SDS-PAGE workflow with 10-12 fractions [More] 1000 1500 3000
11

SILAC workflow (12 fractions)

(price is for analysis of one H+L mix)

 

quantitative proteomics of complex samples from mammalian cell cultures; in-solution digestion fractionation and analysis on a top-performance MS; includes labelling control and comprehensive data analysis [More] 1500 2000 3000
12 Silac check labeling preliminary test to monitor label incorporation ;  package price for up to 4 samples [More] 150 250 400
13 SILAC reagents per 2x100 ml (or 2x250 ml) kit including  :  dialysed FBS, Light AA and Heavy AA for preparing 100 ml H and 100 ml L  (250 ml H and 250 ml L) culture media [More] 120 (240) 120 (240) 120 (240)
14 Slice SILAC variant of SILAC workflow based on an extensive gel separation and fractionation (50 slices); yields large scale mapping of protein mobility shifts; main application: "degradomics" [More] 3200 not done not done
15 Multiplex quantitation (iTRAQ)(12 fractions) quantitative proteomics of any type of complex samples ; in-solution digestion and  fractionation of up to 8 samples in one run (price includes 8 samples analyzed simultaneously) [More] 3500 ask us not done
16 Supplement for high resolution fractionation (24 fractions) applicable to SILAC and Multiplex workflows; for very complex mixtures to get the maximum data [More] 1000 1500 not done
GEL-BASED PROTEIN SEPARATIONS AND PROFILING
17 1D gels + Coomassie or Silver staining
(minigels)
simple protein mixtures, sample preparation for MS [More] 60 100 180
18 2D gels (mini or midigels) with Coomassie or Silver detection two-dimensional separation  for general purposes, total protein detection [More] 80 150 250
19 2D gels + Western transfer
(minigels)
specific detection [More] 100 200 400
REVERSE-PHASE PROTEIN ARRAY
20 Study setup includes project discussion , sample preparation of up to 96 samples (incl quantitation), test spotting of a few samples and detection using max two antibodies, various method optimizations. Needs to be repeated if a new batch of samples with significantly different properties (buffer, concentration, origin, preparation protocol,…) is submitted. 1000 1500 2000
21 Antibody tests and validation printing of a limited number of representative samples  on a multi-pad slide and test of specificity / sensitivity of up to 14 antibodies.  Includes detection and quantitation. 300 450 650
22 Antibody tests and validation: supplement for antibodies cost (per Ab) if antibodies are supplied by the PAF (part of our collection); price per antibody. 30 50 70
23 Slide printing (per slide) 1-pad or 4-pad nitrocellulose slide. 40 70 100
24 Slide detection (per slide) detection with 1- (1-pad slide) or 4 (4-pad slide) antibodies. 120 180 250
25 Slide detection; supplement for antibodies cost (per Ab) if antibodies are supplied by the PAF (part of our collection); price per antibody. 30 50 70

 
Protein identification by short LC-MS run: samples, spots from 2D gels or bands from 1D gels of low complexity mixtures are digested and peptides are analysed by LC-MS/MS on a fast gradient.

 
Protein identification by nanoLC-MS/MS (long run) : starting from gel bands or LC fractions, proteins are digested and peptides extracted. The mixture is then separated on a nano-HPLC system on-line to an electrospray mass spectrometer, which isolates and fragments as many peptides as possible during a 30- to 90-min gradient. Collections of MS/MS spectra are used for database search for protein identification. This workflow is used for analyzing simple to medium complexity mixtures (typically 50-100 proteins) as well as for searching for modified peptides (PTMs). It is also recommended for samples from species with uncomplete genome sequence information available.

 
Direct protein identification by nanoLC-MS/MS (samples ready to inject) : same as above but for large projects in which the customer performs sample preparation so that samples are ready to inject. Workflow and final sample quality are subject to test before acceptance


Special data analysis (per hour) : includes all project specific data analysis procedures, such as setup and formatting of a special sequence database (for example organism-specific) or specific quantifications (PTM, label-free or targeted quantitation).


Direct electrospray analysis : a peptide or small protein is analysed directly by electrospray-MS to obtain its accurate molecular weight. Usually works well only for masses up to 30'000 Da. Requires concentrated and detergent-free samples.


Sample preparation (desalting or other ) : whenever necessary, a sample preparation step before MS can be performed by off-line liquid chromatography (reversed-phase or cation exchange) to clean up the sample. Often required for Direct Electrospray analysis.


Large scale sample preparation: in some experiments, for example prior a PTM enrichment step, a large scale sample preparation is needed and requests a specific sample processing.


PTM identification workflow : gel-separated or liquid phase samples are digested. The eluate is analysed by nano-LC-MS/MS to identify a maximum of modified peptides. This is a comprehensive package including, if needed, digestion with two different enzymes (for example trypsin and chymotrypsin) for better sequence coverage and/or MS analysis with alternative fragmentation methods (ETD , ETHCD). Quantitative data analysis is included (up to a certain level of complexity) to compare levels of modification among samples. Notes : an appropriate negative control should be supplied whenever possible.


Shotgun analysis of complex samples : protein mixtures are separated by limited electrophoresis after which 4-6 molecular weight regions are cut and digested. Analysis is performed by LC-MS/MS on every fraction. The resulting collections of spectra are pooled for every sample before database search. Lists of identified proteins for each sample with their scores are subjected to statistical validation and aligned for comparison.
Note : for the analysis of protein complexes, a negative control is essential for background subtraction.


Extended shotgun analysis of complex samples : same as above, but 10-12 molecular weight regions are cut and digested after separation of protein mixtures by electrophoresis.

SILAC workflow : SILAC is an accurate quantitative proteomics technique based on stable isotope labelling with amino acids in cell culture. It is mostly only applicable to mammalian cultured cells but offers great advantages for experiments in which complex purification steps are required to isolate a fraction of interest, as well as for general quantitative profiling. The PAF offers support during the setup of SILAC labelling experiments as well as the full analytical pipeline (including data analysis). However, carrying out cell culture and the first steps in sample preparation remain responsability of the customers. Preliminary in-depth project discussion is mandatory. Contact us for more information.


Silac check labeling: a preliminary test to monitor label incorporation is carried out by migrating test samples on a SDS-PAGE gel and analyzing the trypsin digest of a band by LC-MS/MS.


SILAC reagents: the PAF can provide users with all reagents necessary to SILAC cell culture : special media (DMEM or RPMI), dialysed serum, isotope labelled amino acids. Exact prices are based on amount necessary and isotope labels chosen.


Slice SILAC : Based on SILAC quantitative technique and combined with extensive SDS-PAGE fractionation (50 slices), it allows studying protein processing ("degradomics") by large-scale mapping of protein mobility shifts, in mammalian cultured cells. The PAF offers support during the setup of SILAC labelling experiments as well as the full analytical pipeline (including data analysis). However, carrying out cell culture and the first steps in sample preparation remain responsability of the customers. Preliminary in-depth project discussion is mandatory. Contact us for more information.

Multiplex quantitation (iTRAQ)(12 fractions): iTRAQ labelling is used for multiplex relative quantitation of up to 8 samples in the same experiment. Labelling is carried out at the peptide level after protein digestion and any type of proteomics sample (cell culture, tissue, etc. ) can be quantitated by this technique. The workflow includes data analysis. Preliminary project discussion is mandatory.


Supplement for high resolution fractionation (24 fractions): for very complex samples in SILAC or iTRAQ experiments, additional fractionation is recommended for higher proteome coverage.


1D gels + Coomassie or Silver staining (minigels) : simple separation on standard minigels


2D gels + Coomassie or Silver staining (mini or midigels) : mostly used for preliminary tests to optimize sample preparation and migration conditions. For maximum sensitivity silver staining can be used, but is not recommended for subsequent MS analysis. For midigels, we use precast gradient gels in the second dimension, which provide very good separations despite their relatively small size.


2D gels + Western transfer (minigels): for western blotting applications, 2D separation on a minigel is often sufficient. The service we provide includes transfer onto nitrocellulose, after which the membrane is returned to the user for detection with antibodies.
 

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