You should check your 401K plan to find out if employer matching and/or profit sharing contributions are offered, and if so, what the terms and conditions of the matches are. You should seek to maximize the employer match. One of the advantages of an IRA is that you have more investment choices than with a 401K, however there are numerous disadvantages, including that you may not be eligible for a deduction depending on your income. More details regarding this can be found here: http://www.irs.gov/Retirement-Plans/2015-IRA-Deduction-Limits-Effect-of-Modified-AGI-on-Deduction-if-You-Are-Covered-by-a-Retirement-Plan-at-Work I recommend that you consult with a financial adviser for a more detailed analysis of your particular situation.
In a perfect world, you would utilize both. One main benefit that a 401k has over an IRA is the ability to put a much larger amount into the 401k. You can defer up to $18,000 into a 401k ($24,000 if you are 50 or older) in 2015; whereas, you can only deposit $5,500 ($6,500 if you are 50 or older) into an IRA. If you mean that you are only really getting started on saving for retirement in your 40s, you will probably need to save as much as possible every year in order to build up enough for retirement. I would suggest maxing out your 401k with $18,000 of salary deferral (if your company offers a match, all the better) and maxing out a Roth IRA with $5,500. One caveat is that if your income is too high (see here for the amounts: http://www.irs.gov/Retirement-Plans/Amount-of-Roth-IRA-Contributions-That-You-Can-Make-For-2015) then you may not be able to contribute anything to a Roth, at least directly. If you max out those two sources and still have money to save/invest, then you can look at an after-tax brokerage account to save even more. Another thing to think about in all of this if whether you have an adequate emergency fund ("adequate" can vary from person-to-person, but a good starting point is to have at least 3 months worth of monthly expenses set aside in a plain savings account that is easily accessible and not subjected to the volatility of the markets - perhaps 6+ months worth if you have a family and/or are the sole earner, etc.). As Dmitriy suggested, talking with a qualified fee-only financial planner might not be a bad idea since s/he could review your entire situation and help you structure a plan to fully maximize things. Best of luck.
If your employer offers a matching contribution to your 401k, do take advantage of that. You can also set up and contribute to an IRA for more flexibility, especially the ability to choose providers with better investment options and/or lower fees. In regard to what to invest in, I recommend talking to a qualified financial advisor who can help you choose the right investment options to fit with your goals.
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