Proteomicss Facility

Users need to register the samples in the portal.
A clear description about the samples/experiment is necessary.
- Source - cell line/tissue/E. Coli/yeast etc.
- Brief description - Sample concentration i.e. amount of total protein taken for trypsin digestion, Desalted (method), Cellular extract or Immunoprecipitated samples etc.
- Kind of analysis required - mass detection, protein identification, protein quantification, protein sequencing etc.
LC gradient/mass analysis protocol - facility will decide the protocol depending on the sample description provided and experimental need. Users are requested to discuss with the facility for special requirements.
After sample registration, an automatic email goes to the PI with registration detail (link) for confirmation. PI needs to finally submit the samples to the facility by pressing the 'approval' button provided in the link. After approval, all samples are provided with unique sample numbers and queued.
Current sample running status in the Mass Spectrometers will be visible in the portal allowing the user to anticipate the waiting-time.
An automatic mail will reach the user once sample run is over.

For mass determination in MALDI TOF-TOF /Finnigan LTQ - a batch of 30 samples
For proteomics experiments (sequencing, protein identification and quantification) in OrbiTrapVelos - a batch of 20 samples
For proteomics experiments (sequencing, protein identification and quantification) in Q-Exactive - a batch of 20 samples
Every user can submit samples once in a month.
Facility may allow consecutive samples from the same user in case of no registration from others.
For special considerations - please discuss with the facility.
Control proteome digests will be run before and after all submissions. Control data will be provided upon demand.
Raw data will be saved in the facility for one month after the experiment.

Users are requested to provide enough information/justification about their experiments. Facility may postpone the experiments if sufficient information is not available.
Based on the experience of Proteomic facility, the common problem that leads to failure of sample run or spoilage of the columns is poor quality of samples. Poor quality is with respect to improper peptide concentrations, poor digestion and presence of contaminants.
Unsuccessful digestion/desalting and excess sample concentration does not lead to failure of your run only; this affects all the following runs as well. Sometimes, this may destroy the reverse-phase column. Please note, a regular-quality (5 micron) column costs ~ 35000 INR; a better-quality column (3 micron) costs ~80000 INR.
Users are requested to provide high-quality samples. Samples must be efficiently digested and desalted to avoid unsuccessful runs. Too high or too less sample concentrations also lead to failure often.
Please follow the guidelines for sample preparation provided in the portal. Training classes on sample preparation protocol will be also arranged regularly.
Training classes on analysis protocols will be arranged regularly. For troubleshooting, please ask the facility staff to help you in their free time.
For any clarification, please discuss with the facility.