Does gross adjusted income include payroll deductions and retirement savings?

I have a slightly odd situation where I have to make quarterly estimated tax payments on my current income (taxable income from Grants or Scholarships), but starting in September I will have a contract position with standard witholding and payroll deducted insurance premiums, 401K, etc. I was able to calculate estimated witholding and subtract that from my quarterly payments, but my state of Maryland tax estimator has no place to account for payroll deductions like health insurance premiums or for retirement savings contributions, and I don’t see either category listed as qualifying "subtractions." In the federal worksheet, there were dedicated boxes for this stuff.

My questions is, are payroll deductions and/or personal contributions to a 401K or traditional IRA (withing the respective contribution limits) still included in my federal gross adjusted income (estimated). Or is the GAI my wages and grant income minus those things? It makes a pretty substantial difference in how much I need to pay.

Sorry if this is super basic. It’s the reality for working scientists in the US. You’re paid on grants and scholarships with no benefits for so many years of adulthood. The next thing you know you’re 33 years old with a PhD and no clue how regular taxes work.