Frequently asked questions

  • How do I submit samples to the Mass Spectrometry (MS) facility at IIT-Bombay?
    First, please provide your details and that of your samples on the this link and click Submit. A PO will be generated; you can download it, get the signature and stamp of your HOD/PI and send a scanned soft copy to massfiitb@gmail.com and a hard copy couriered to us. Please make sure all the details are correctly and completely entered, otherwise your sample submission will get not accepted at our facility. Our team will scan your document and assign a date as per your position in the queue. Please make sure that your samples reach us before that date.
  • What precautions should I take when sending my samples?
    Make sure you send your protein sample in a well-sealed eppendorf tube so that there are no leaks. Make sure to send us complete information on what buffer it is dissolved in or was dissolved in before drying the pellet. You can also send us protein bands cut out from gels; however they must be Coomassie-stained (preferred) or MS-compatible silver stained gels. Make sure all buffers, waters and other chemicals that you use are MS-grade only.
  • How much sample should I send?
    For tissue samples, we recommend sending a minimum of 100 mg of total tissue.  In the case of cultured cells, please send at least 105 cells in pellet form or in suspension.  For serum samples, please send a minimum of 200 ul crude serum. If you are sending us purified protein, please send us a minimum of 100 ug protein/sample. For clinical samples please do provide the IEC documents and biosafety precautions also.
  • What are the charges for the Mass Spectrometry services at your facility?
    It depends upon what services you are opting for in addition to the Mass Spectrometry Analysis. We provide value-addition to our customers, whereby they can opt for a plain MS analysis or can request for upstream sample preparation such as protein extraction, protein digestion, quality control checks, protein fractionation, 2D-electrophoresis with band excision, iTRAQ labelling of peptides, etc. In case you still have some questions or comments, please feel free to contact us at sanjeeva@iitb.ac.in
  • What is the turnaround time for your services?
    It depends on what services you have opted for. If you include all the steps from protein extraction to complete MS/MS data analysis with report, it could take 1-2 weeks depending on the complexity of the samples. If there is an additional need for troubleshooting certain steps, it might even take a little longer. At every step, our application scientist will be in touch with you with an update on your experiment. We will also update you with sample queue and possible time for sending your results
  • What precautions should I take with my sample if I want to opt for in-solution digestion and/or iTRAQ labelling services?
    Since these applications are very sensitive to contaminants, we insist that the quality of your protein as well as the buffer it is in, is of the highest quality. Our recommended buffer is 0.5 M Triethylammonium bicarbonate buffer (TEAB) of the highest quality MS-grade. However, you can also submit your samples in any buffer of your choice but we will have to exchange the buffer before carrying out further analysis.
  • How can I perform protein sample clean-up in case my proteins contain detergents, salts, or any other contaminants?
    It depends on the stage at which you want to perform the sample clean-up.  If you are interested in only one particular protein, you can run your protein mixture on a gel, cut the band of interest and then purify it in the buffer of choice. Another option is to use precipitation methods with TCA-Acetone or TRIZOL. However, do make sure that the resultant pellet can be redissolved in the appropriate buffer. You can also use hydrophobicity-based reverse-phase chromatography or strong cation exchange chromatography to clean-up your proteins. There are ready-made columns such as Zip-tips that are available for such purpose.
  • How will I receive my data?
    We can provide data in many formats, depending on what you have chosen for data analysis while placing your order.  The minimum we do provide is an Excel- sheet with a list of identified proteins, their corresponding accession numbers to an appropriate database (e.g. Uniprot). We can also provide sequences of identified peptides, peptide scores, sequence coverage, position of the peptide in the protein, annotated spectra for all peptides, etc.  We can discuss this with you before you place the order so that we better understand your requirements.
  • I am publishing a paper that includes data acquired from your facility – what should I include in my methods and how should I acknowledge the facility?
    In case you are writing a paper with data generated from our facility, you can simply acknowledge the facility.
  • How much background information would you need for the protein identification/analysis, e.g., species information, proteomic or genomic information?
    The more information you can provide us, the better and with more confidence we can help you with the identification and analysis.
  • Why do I see a lots of keratin in my proteins? Where do they come from?
    Keratins are introduced during sample preparation and are contaminants from your fingers (always use gloves when handling protein) or from dust particles in the air (make sure you process your samples in a dust-free, clean environment).  Always make sure that you use MS-grade chemicals and your buffers are 0.22 uM filtered and made up in autoclaved MilliQ water.
  • Why should I opt for your additional services such as protein extraction, digestion, labeling etc.?
    We certainly don’t offer this as a routine facility service. If you have the appropriate infrastructure and capability in your facility to carry out these steps, please do so. If you have any trouble in doing these steps in your laboratory, we could help you by offering additional services.