What's the negatives & positives of creating a mobile app with different functionalities from the web app?

I'm creating a marketplace website.

I was thinking keeping the marketplace exchange on the web app and a much simpler version on the mobile app providing only profiles with some other cool perks you can't do on the website.

Typically your web application is full featured, giving you every possible capability on the website. Mobile applications are usually created for convenient access to critical features that you may need to get at from anywhere. For a marketplace exchange it may be convenient access to messaging, or ability to look at products you are selling or buying and do things that may have time consequences if you can't get to a computer in a couple hours.

Everything should be big and easy, worst case scenario if you need to get to a feature you can access the web application. In the FreshBooks mobile application, for convenience features that they didn't offer on the app they provide a link in the app to open the web application in Safari and you can use it in the browser. Sounds a little clunky but they actually did a decent job with it.

37 Signals has recently been posting about the process of creating their iPhone application for their primary product Basecamp that is worth reading over:

http://37signals.com/svn/posts/3438-drawing-the-nativeweb-line-in-basecamp-for-iphone http://37signals.com/svn/posts/3439-design-decisions-projects-on-basecamp-for-iphone http://37signals.com/svn/posts/3432-why-i-loved-building-basecamp-for-iphone-in-rubymotion In general I'm not sure I would offer features that are only in the mobile application. I would be irritated if I'm at my computer but needed to look at or check something out and had to get my phone out to access the app and take care of it there. But "perks" may not necessarily be features, perks could be some simpler charts / graphs that are nicer when viewed on a phone or something like that I guess.

Good luck.