For submitting the sample first you need to login into MS-facility sample submission online form (please register if you are not a user). Please raise a request and fill-in all the possible details. The more details you provide us, the more helpful we can be. Once you fill the form we will get back to you about the feasibility of your request at our facility. Only after this point will we ask you to send the samples.

We would suggest following aspects;

a) Clean the whole gel running apparatus, use fresh glove in all the steps and maintain clean surfaces all throughout the process !!!!!

b) Use freshly prepared buffer and stains do not re-use.

c) While loading the sample over gel, Isolate the sample from any other controls (such as whole cells lysates etc if any) to avoid cross contamination. Preferably run samples in a separate gel with ample gap from marker (2-3 lanes). In case you wish to run a single gel for all of your samples, maintain gap of 2-3 lanes between sample and control. Never leave a lane empty, rather load similar volume of sample loading buffer. This will help in fine streamlined sample bands.

d) You must note the total protein loading amounts (Provide the information to us)

e) Stain the gel and capture an image. (Provide the information to us)

f) Cut the band only after imaging. Cut necessary bands using fresh sterile one time use scalpel blade on a clean surface in the laminar hood.

g) Provide the band to us in clean eppendorf tube suspended in MS grade water.

We would accept centrifuge tubes of ‘Eppendorf’ make. The reason for this is that they provide least chemical background and minimum leaching from the surfaces.
If your sample is a gel piece, then please send it immersed in MS grade/LC grade/Double distilled water through courier/post. You may also deliver it by person after contacting us and arranging a convenient time to meet facility personnel.
If your sample is in solution, please ensure you send it with dry ice when you are sending the same over post. We would not be in a position to help you with bad results obtained due to improper storage/transport of the samples.
If your sample is dried powder or pellet please contact facility personnel. It is important to contact us because sample may have problems related to dissolution depending on the way it was precipitated.

We require the sample quality to be high for this particular service. We require minimum of 2-3 microgram of the protein suspended in 8-10 microleter of buffer. It is mandatory that the buffer in which you submit the sample, is free of any chemicals such as urea, triton-X, CHAPS, SDS or any other related chemicals. We can only accept your sample if all criteria are met.

We do not perform this under our services. We recommend the users to perform this before submission of the sample. Moreover, we are not experts in this, because it may vary from sample to sample and case to case. However, we have observed some of our users using some of the methods such as running a SDS-PAGE, passing through molecular weight cut-off columns, using some precipitation method (please perform this if you can re-dissolve the resultant pellet) etc.

It depends up on the number and nature of analysis you are interested in. Ideally, molecular mass measurement using our Q-TOF MS requires minimum 2-3mg of total protein which is totally free of chemicals such as surfactants and salts etc. For gel separated proteins, we are OK with a gel piece which is faintly stained with coomassie.

Please send your samples with proper cooling condition (if it is in buffer/solvent preferably send it with dry ice at -20 C. If it is power/gel piece at 4C) to following address:

Dr. Vikas Kumar / Mr. Prashant
Mass Spectrometry Facility - Proteomics Unit
Centre for Cellular and Molecular Platforms,
National Centre for Biological Sciences (NCBS-TIFR),
GKVK Post, Bellary Road, Bangalore 560065

Please mention "Requires COLD STORAGE upon receiving" on the cover of the package.

Species information is the heart of bottom-up proteomics work flow for identification of proteins of interest. Hence, if you know the species/genera/organism please provide the info on the service requisition form. If you know but you are not able to share this information due to confidentiality issues, we would perform a general search of your results on Swissprot database and provide you the list of proteins. In case you are aware that your protein is from an unannotated organism, please get back to us.

We perform analysis of your samples over Nano-LC system which has a Nano-column and a chip based nano spray unit attached to it. The advantage of this system is, we need very minimal amount of the sample. By keeping the system setup in mind, we can’t overload the system with highly complex and highly concentrated samples. This will hamper our system and your analysis too. An estimate of the sample load provided by you will help us to back calculate approximate amounts of sample to be loaded on the column. A gel picture is a secondary confirmation of the amounts. By looking at the stain intensity as well as bands we can get a gross idea about complexity of the sample. This will help us to judge and assign a better separation gradient for your sample.

Yes, but make sure the sample is salt free. You would also need to provide information about the amount of sample you will send and its molecular weight. If your sample is dried pellet please contact facility personnel as sample may have problems related to dissolution depending on way it is precipitated.

We prefer Coomassie stained gels, but accept gels stained with MS compatible silver stain. Through our prior experience we have learned that silver stained gel pieces do not obtain better results in general than Coomassie-stained gels. This may be attributed to cross linking within proteins and also with gel due to developing agents such as formaldehyde and glutaraldehyde etc used in the process. Even after this if you require the sample to be analyzed, kindly fill the form and get in touch with us. Whenever you fill a form for a silver stained band, please provide us the stain details with protocol followed for staining and de-staining.

Following are few review articles we would suggest you to read, which will help you to understand the mass spectrometry and proteomics.
1) Mass spectrometry-based proteomics (PMID:12634793)
2) Proteomics by Mass Spectrometry: Approaches, Advances, and Applications (PMID:19400705)
3) The pros and cons of peptide-centric proteomics (PMID:20622832)
4) Mass spectrometry based functional proteomics: from molecular machines to protein networks (PMID:17901870)

It is a difficult question to answer. Generally, results from routine molecular mass measurement will be delivered within 1-2 days. The other processes such as in-gel digestion and protein identification will need minimum 1-2 weeks.

We follow different fee structures for internal academia, external academia and commercial users. The cost may also differ depending on particular research question you ask us to solve for you. For further details please write to Mr. Mohan Sridhar at mohans at ncbs dot res dot in.

The data on mass measurement will be sent as PowerPoint slides and proteomics data will be sent as Excel sheets. About raw data, we prefer that data is not given out of our hands. If you feel it is very necessary under special circumstances, kindly get back to us and we will guide you through our policies of raw data sharing.

It is mandatory to acknowledge the MS-Facility in your achievements. In case of companies or organization which provides the data to the third party, please check our website at http://www.ccamp.res.in/molecular-characterisation-proteomics.html for our Raw Data and Data Storage policy. It is a must to also formally acknowledge the facility in writing in the case of providing our report to a third party and also declare us as a preferred MS partner of your company/ organization.

Yes we can do it. But it takes quite different way of analysis than that of routine bottom up proteomics analysis of searching MS data against database of known set of proteins. The other way can be termed as homology driven proteomic analysis. In this approach we process your samples with ‘Eagle eye’ followed by sequencing and identification by ‘Pepnovo’ and ‘MSBlast’. This analysis will end up providing a list of proteins which are originating from phylogenetically nearest Sequest organism. More of the details can be obtained from following article;  “Protein Identification Pipeline for the Homology Driven Proteomics” Magno Junqueira et al.  Journal of proteomics, 2008. (Pubmed ID: 18639657)

A work order is request made from your Institute/Organizations Purchase Department for the service we are providing. It needs to be made against the quotation that we provide.
Click here for the work order template.