If you are covered by some direct action of the web spam team which has an unswerving effect on the ranking of your site, then you can check in webmaster tools whether there is any cloaking or some crawl error, like forgetting to remove the no index tag from a site and thereafter try to rectify the problem.
In reality, google webmaster tools do not concentrate on or think about algorithmic penalty. The web spam team writes different codes which go into holistic ranking that they do. So, you cannot specify whether an algorithm is affected and you call it a penalty. Web spam teams usually makes general quality changes and not specific to web spam and vice versa.
However, if the team finds an algorithm effect might have a pretty big impact, they try to notify the users. For example, you can take the penguin algorithm which is targeted towards web spam or panda algorithm which is targeted towards the quality content on the web. So, whenever a large change takes place, webmaster tools announce the change followed by the area you have to look into.
Panda algorithm has become more integrated with indexing so as to reduce the jolting impact of indexing. And it changes the index at a regular basis. Whereas penguin algorithm start rolling at a discreet time which becomes difficult to ascertain.
In reality if your page is not ranked where it is ought to be, then it might be difficult to know whether it is part of ranking or penalty. But since it is algorithmic, if you modify your site, the possibility of the algorithm to re- score or re- index your site is high. It is difficult to distinguish a penalty of algorithm but as you change your site, you can process the algorithm simultaneously to regain ranking position.