Budget Development

Graduate Student Compensation Increase - Effective 7/1/2022

Updated Federal Indirect Cost Research Rate For Competitive Grant Applications - Beginning 1/1/2022

Additional Federal Indirect Cost Rates Change Beginning - Beginning 1/1/2022

Billing Compliance and Medicare Coverage Analysis

A Medicare Coverage Analysis (MCA) is required for research studies which may bill protocol required routine care services to patients or third-party payers (medical insurance companies). The MCA assists ISMMS in meeting the Centers for Medicare and Medicaid Services (CMS) billing compliance requirements for routine care in research. Learn More

Training and Education

GCO Classes

The GCO offers the following classes to assist investigators and study teams with budget development related to sponsored projects:

  • GCO 201: Basics of Sponsored Projects Budgeting
  • GCO 202: NIH Modular Grant Budgets
  • GCO 203: Budgeting Direct Costs on Federal Awards
  • GCO 204: Budgeting Indirect Costs on Federal Awards
  • GCO 205: Applying the Updated Federal Indirect Cost Rates
  • GCO 301: Preparing Grants with Subawards

Learn More 

MCA Mandatory Training

Principal Investigators with studies that require a Medical Coverage Analysis (MCA) are required to complete the Clinical Research Billing Rules for Investigators training in PEAK before final approval is granted from the IRB.

NIH Instructional Material

The NIH has a wide array of videos, webinars, podcasts, and other instructional materials – Learn More

Budget Templates

GCO provides templates to assist faculty and staff develop budgets.

Note: Use of these templates is not required.

Billing Compliance and Medicare Coverage Analysis
A Medicare Coverage Analysis (MCA) is required for research studies which may bill protocol required routine care services to patients or third-party payers (medical insurance companies). The MCA assists ISMMS in meeting the Centers for Medicare and Medicaid Services (CMS) billing compliance requirements for routine care in research. A billing grid is developed that can assist in budget negotiation by identifying which items are research, which are SOC and what may be billable to insurance. Learn More

Indirect Cost Rates


Indirect costs (also referred to as “Facilities and Administrative (F&A) costs”, or “overhead”) are costs that cannot be readily identified with an individual project or program. Indirect costs reimburse the ISMMS for administrative, space and other expenses.


Indirect costs are charged to sponsored projects from extramural funding entities, gifts, donations and others. For a summary of indirect cost rates for various funding entities, refer to the following:

Indirect Cost Rate Waivers: If the funding source will not pay the specified rate, a waiver is required from Chief Financial Officer (CFO) or the Dean.  If the waiver is not granted, the department will need to supplement the difference. Requests for indirect cost waivers should be made in writing by the chair or departmental administrator and submitted to Stephen Harvey, CFO.

For more information, including charges not subject to indirect costs for grants and contracts refer to Financial Memorandum #157: Policies and Procedures for Charging Indirect Costs to Sponsored Projects Received from Extramural Sponsors, Gifts, Donations, and Other Receipts.

Direct Costs


Direct costs are those that can be specifically identified to the sponsored project award and are allowable under the sponsor’s guidelines. They typically include:

  • Compensation of employees for time and effort devoted specifically to the execution of the award’s objectives
  • Equipment and other approved capital expenditures
  • Consultants
  • Material and Supplies
  • Travel
  • Patient Care Costs
  • Subawards
  • Other expenses incurred specifically to carry out the proposed work

Fringe Benefit Rates


Fringe benefits are non-wage compensation items such as medical and dental insurance, retirement benefits, disability insurance, and social security pension that are provided to employees.


Sponsored Projects Finance (SPF) negotiates fringe benefit rates with Department of Health and Human Services (DHHS) annually. Fringe rates (federal or non-federal) are required to be applied to personnel (Faculty, Staff, Postdocs, and Students) salaries when developing budgets.

Budgeting for ISMMS Faculty and Staff

Salary Restrictions for Principal Investigators and Senior Personnel

HHS/NIH Salary Cap

The Department of Health and Human Services (HHS) /NIH has a salary cap limitation on direct salary for individuals under NIH grant and cooperative agreements. If you are applying for a Department of Health and Human Services (HHS) sponsored project and your institutional base salary (e.g. $200,000) is greater than the NIH / HHS salary cap, use the latest salary cap rate that is listed on the Administration Information Sheet.

Faculty Effort

Refer to the following policy and resources when preparing your proposal:

Budgeting for an ISSMS Faculty Member with a Veterans Affairs (VA) Appointment


Mount Sinai faculty members working on a research project with an appointment at a Veterans Affairs (VA) Medical Center are required to document VA effort commitment.


Refer to the GCO documentation:

Application Requirements: Verification of approval from the appropriate JJPVAMC administrative officer must be obtained confirming that VA funds will cover the cost of employees’ effort or other than personnel expenses rather than the sponsored project budget. Email documentation is required to be uploaded into the Internal Documents tab of the InfoEd application.

Non-MSHS faculty and staff working on projects should be budgeted as consultants or under a subaward budget.

Budgeting for Students and Post Graduates

Detailed information regarding eligibility requirements, stipends, tuition and fringe benefits can be found in the GCO’s handbook, Guidance for Including Students and Post Graduates on Federal Research, Fellowship, and Training Grants.

Graduate Student Total Comp (Effective July 1, 2022)

Budgeting for Administrative and Clerical Staff


According to the Federal Uniform Guidance, administrative and clerical salaries should normally be treated as indirect (F&A) costs and therefore should not be charged to individual grants and contracts.


However, direct charging of the salaries of administrative and clerical staff may be appropriate to a Federal award if ALL of the following are met:

  1. Activity must be integral to the project or activity;
  2. Individuals involved must be specifically identified with the project or activity;
  3. Such costs are explicitly included in the budget or have the written approval of the Federal awarding  agency (unless the funding agency has specifically waived the requirement for prior approval);
  4. The costs are not also recovered as indirect costs


For more detailed information and a list of examples, refer to Charging Administrative and Clerical Salaries to Federal Grants and Contracts (171).

Budgeting for Consultants

When preparing budget proposals for consultant services it is important that the contractual relationship is properly classified. There are important differences between subawards, consultants and vendor relationships relating to F&A costs as well as compliance requirements.

Refer to the following documents to determine your contractual relationship:

Consultants typically will charge a fixed rate for their services that includes both their direct and F&A costs. The budget does not need to include

NIH Grant Application Tip - Letters of Support from Consultants 
Remember to include letters of support from consultants if required.  Review the funding agency’s instructions for more information.

Departmental Requirements


Consult with your department administrator for specific budget requirements and procedures. Some items to discuss include cost sharing, effort and salary verification. Verify base salary for all personnel with your departmental administrator prior to finalizing and submitting your InfoEd application.


Refer to the Departmental Pre-Award Contact List.

Research Patient Care Costs

Billing Compliance and Medicare Coverage Analysis
A Medicare Coverage Analysis (MCA) is required for research studies which may bill protocol required routine care services to patients or third-party payers (medical insurance companies). The MCA assists ISMMS in meeting the Centers for Medicare and Medicaid Services (CMS) billing compliance requirements for routine care in research. Learn More


NIH provides funds for research patient care costs under grants and cooperative agreements. Research patients may receive routine services as inpatients or ancillary services as either inpatient or outpatient subjects/volunteers/donors in a hospital or clinic. Refer to the NIH Grants Policy for definitions, guidelines and allowable costs relating to research patient care costs. Note, research patient care costs do not include costs such as subject compensation and travel. These costs should be included under “Other Expenses”. 


Clinical procedures for federal, state and other non-profit funding agencies should be budgeted at the federal research rates. Industry funded studies should use Industry research rates. To access these rates, consult with your department research administrator and/or use the following fee schedules listed below.

Institutional Fees

Service Fee
BioMedical Engineering and Imaging Institute (BMEII) Resource Fees
Clinical Research Unit (CRU) Fee Schedule
Investigational Drug Service Usage Fees
ISMMS IRB Fees Information for Sponsored Research
ISMMS single IRB (sIRB) Fees IRB@mssm.edu
Medicare Coverage Analysis (MCA) – Non-profit studies Fee Waived
Medicare Coverage Analysis (MCA) – For-profit Funded studies FACTS Fees

Research Fee Schedule Contacts

Department Contact
Anesthesiology James Leader
BioMedical Engineering and Imaging Institute (BMEII) BMEII Director
Biorepository and Pathology CoRE Rachel Brody, MD, PhD
Cardiology Debra Fitzpatrick
Dermatology Giselle Singer
Hospital Fees Inna Bender
Medicine Divisions Michele Cohen
Neurophysiology Lab Mary-Catherine George
Ophthalmology Jill Slutsky-Sanon 
Pathology, Molecular and Cell-Based Medicine
Clinical Labs
Beverly CooperClinical Labs Price List
Pathology, Molecular and Cell-Based Medicine
Transfusion Medicine and Cellular Therapy Laboratory
Jeffrey Jhang, MD
Transplant Brandy Haydel
Translation Fees Language Assistance Program (LAP)

Single IRB (sIRB) Fees – Multi-site Research


NIH has issued a policy (NOT-OD-16-094) requiring domestic multi-site studies conducting the same protocol involving non-exempt human subject research to use a single IRB (sIRB). Typically, costs associated with IRB review are not allowable as direct charges to NIH-funded research unless such costs are not covered by the organization’s F&A rate. However, the NIH has issued a policy (NOT-OD-16-109) that outlines sIRB activities which may be charged as direct costs.


If an ISMMS investigator is the prime applicant of a NIH grant or contract conducting a mult-site clinical trial they should contact the Mount Sinai PPHS office early on when to discuss:

  • If they plan to have ISMMS serve as the sIRB (refer to page 3, of GCO’s Guidance Document on NIH’s sIRB policy for specific criteria)
  • Estimated ISMMS IRB fees for the grant budget (if ISMMS IRB will serve as the IRB of record)
  • Selection of an alternate SMART or commercial IRBs (see TIN services)


Contact the PPHS office at irb@mssm.edu.

If the ISMMS IRB will not serve as the IRB of record, fee information for conducting the sIRB will need to be obtained from the alternate IRB.



Outgoing Subawards (ISMMS is the Prime Institute)


When ISMMS is the prime institution on a sponsored project application, each sub-awardee or sub-recipient institution is required to submit subaward documentation including a budget and budget justification to ISMMS. These documents are required to be included in the GCO InfoEd application submission.


The GCO InfoEd application requires at minimum, as much budget information and documentation as the extramural funding agency requests. For detailed guidance on developing a budget and the InfoEd applications requirements, refer to Subawards: ISMMS as the Prime Institution.

NIH F&A: Refer to the NIH F&A Consortium/Subaward guidelines – NIH Develop Your Budget

Incoming Subawards (ISMMS is the Subawardee)

When ISMMS is the sub-awardee or sub-recipient on a sponsored project application, the GCO InfoEd application requires as much budget information and documentation as the prime institution requests. For detailed guidance, refer to  Subawards: ISMMS as the Subawardee.


For NIH grants, equipment is defined as an item of property that has a unit cost $1,500 or more and a useful life of at least one year.



GCO Contacts 
GCO Assigned Departmental Grants Specialist

For-profit Clinical Research Budget Development

Department Contacts
Departmental Pre-Award Contacts

Research 411 Portal

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