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When queried Salesforce using DescribeSObject API call, we get the desired fields list. But when queried through Force.Com explorer I am unable to read the values. Can I difference between using DescribeSObject call and Force.com explorer?

Few fields are managed-installed , few standard and few custom fields

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It may have something to do with the API version. The Force.com Explorer is not up to date with the latest API version (stopped at 19.0 I believe), so if an object or field is only available with a later API version than the Force.com Explorer uses you would not see it. For example, the ChatterActivity object is only available in API Version 23.0 and later, so you can't see it with the Force.com Explorer, whereas the ContractFeed object is available in API Version 18.0 and later and you can see it.

Another possibility, is that the profile of the user connecting through the Force.com Explorer has different FLS than that of the profile of the user using the Describe.

Note that support for the Force.com Explorer has been abandoned, so in lieu of it being open sourced and updated you won't ever be able to see it. The question that I linked to has very good alternatives.

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