Once you have produced a list of potential protein biomarkers from your LC-MS/MS experiment, online tools can be very helpful in working out which ones should be prioritized for further study. Typically, the logic is that potential biomarkers that have something in common, such as being members of the same biochemical pathway, are more likely to be real. Many online tools exist to help establish relationships between potential biomarkers; most of these will also help in understanding the protein's biological function. I'd suggest trying STRING and DAVID, both of which aggregate information from a number of sources.

http://string-db.org/

http://david.abcc.ncifcrf.gov/

For identification of protein biomarkers from LC MS/MS data use Mascot software, the benchmark for identification, characterisation and quantitation of proteins using mass spectrometry data.

http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=SQ

MaxQuant (http://www.maxquant.org/)  is a freely available software for protein identification and quantitation from LC-MS/MS data. It also comes with an add-on software - Perseus - that helps with normalization, statistical analysis and biological annotation of the data. It is not online per se, but can be downloaded and installed. For usage please look up the videos from the yearly MaxQuant summer school on Youtube.

Thank You sir for your suggestion 

I tried MaxQuant (Version 1.5.0.25) .  My raw data is in .wiff format. and MaxQuant (Version 1.5.0.25) have facilities to process .wiff file . when I tried to process the file after some time its showing some error and the processing interrupted in between.  

Dear David thank you for your suggestion 

can I process the raw data using those online tools mentioned by you. 

Known problem with MaxQuant 1.5.0.25, and the MPI group who write the SW are aware of it. I assume your data are from an AB SCIEX QToF (4600 or 5600)? If it is QTRAP data then MaxQuant will probably not work for you. For a fix to the QToF problem, look to the MAxQuant Google Forum - should come up some time soon I hope (I also run a 5600).

My data are from AB SCIEX QToF 5600 and its iTRAQ labelled sample. 

thank you for information.

For an existing dataset you might also look at AB's ProteinPilot software. You can download a free 30-day trial license from their webpage. It will process for 30 days, after that you will still be able to view results. It does not have additional functionality for statistical analysis or functional annotation though. Current version is the 4.5 beta available on the website.

Subas, I misunderstood your question. The tools I mentioned (DAVID and STRING) are useful for tasks such as prioritizing potential biomarkers for further work; for example, you might use them to look for relationships between a set of proteins found in your iTRAQ experiment to have undergone a two-fold or greater change in relative abundance. If you're looking for online tools to identify peptides from tandem mass spectrometry spectra, there are a number of options. Mascot has already been mentioned, but you need a subscription to search large datasets. The best free option is probably using The Global Proteome Machine. This searches your data using X! Tandem, which is a good choice. Before upload you need to convert your proprietary vendor raw data format to an open format. ProteoWizard includes tools for this purpose if you can't export mzXML or mzML from the AB SCIEX software. An alternative that you run on your own computer, but which is open source and a free download, is the Trans-Proteomic Pipeline (TPP). I'm pretty sure this includes conversion tools for the AB SCIEX raw data format. The TPP includes X! Tandem and Comet for peptide identification.

http://thegpm.org/

http://proteowizard.sourceforge.net/

http://www.proteomecenter.org/software.php

Thank You Mr David for your valuable suggestion . I will try and let you know. 

Thank You Mr Lenz for information