NIH Proposal Guide


Proposals and the budgets for projects being submitted to the National Institutes of Health (NIH) should be developed by principal investigators (PIs) with the assistance of their department and/or Office of Pre-Award Services (OPAS). Proposals must be submitted to OPAS following the 5 day proposal submission procedure. Following the 5 day proposal submission procedure, the proposals may include draft technical sections (Research Strategy, Specific Aims, Project Summary/Abstract, and Bibliography/References Cited documents) but complete in all other respects. Final versions of the Research Strategy, Specific Aims, Project Summary/Abstract, and Bibliography/References Cited documents should be provided to OPAS no later 48 hours before the NIH deadline. Proposals are routed to relevant signatories and finally to OPAS for review prior to the official submission to the NIH.

OPAS reviews each NIH proposal for compliance with both sponsor and University policies. OPAS also reviews the proposal to verify that only allowable costs   have been requested and only approved University and/or other vetted personnel such as subcontractors, consultant, fee for services providers are included in the proposal. For a review of allowable costs on Federally-funded projects please see Cost Restrictions on Federally Funded projects .

PIs seeking assistance with how to prepare an NIH proposal should contact their department or OPAS proposal and budget development services. However, PIs should feel free to contact James Warren (College of Natural Science) or Sara Santos (all other schools and colleges) during any point of this process for clarification, guidance, or consultation.

List of Contents:

NIH Proposal Submission

Prior to official submission to the NIH, proposals must be submitted to OPAS for review and institutional approval. Currently, you must use one of these submission options to access the application forms for an NIH opportunity:

  1. Use Kuali for submissions (the UMass Amherst system that assists with building and routing proposals to OPAS).
  2. Use the NIH ASSIST system to prepare, submit and track your application online.
  3. Go to to download an application package to complete the application forms offline or create a Workspace to complete the forms online; submit your application to; and track your
    application in eRA Commons. (Top)

NIH eRA Commons

When submitting a proposal to NIH, NIH requires the Principal Investigator to have an NIH eRA Commons account.  The NIH eRA Commons account allows the PI to submit an application via OPAS and review and administer certain aspects of their own NIH submissions. To register, PIs should contact James Warren (College of Natural Science) or Sara Santos (all other schools and colleges) with the information below:

  1. First Name:
  2. Last Name:
  3. UMass Amherst Email:
  4. Type of account needed (i.e., PI, Postdoc, Graduate Student, Assist):

After your account is created, you will receive an automated “Account Created” notification email from NIH containing the username and a randomly generated password. Please activate your account and populate your profile as soon as possible.

When submitting a Progress Report to NIH, NIH requires associated undergraduate and graduate students on NIH-funded projects for at least one person month or more to have an NIH eRA Commons account. Follow the same instructions above to request the creation of an account for undergraduate and graduate students who participate in NIH-funded projects. (Top)

Changes to NIH Policy and Procedures

To stay up to date with important changes in NIH policy and procedures, PIs and Business Managers may want to subscribe to the NIH Guide for Grants and Contracts or visit OPAS’s website. (Top)

Consultant, Subcontract, Fee for Service or Other Significant Contributor?

At times it can be difficult to tease out a participant’s role in your proposed project.  It is important that the correct agreement determination is made early in the process of preparing a grant application, as indirect costs and monitoring requirements for these types of agreements vary and will impact the grant budget and, in some cases, the grant narrative.

Before entering into a relationship with another organization in relation to NIH-funded research in which the other organization will provide services or programmatic work to UMass Amherst as the prime recipient of funding, a determination must be made as to the nature of the legal relationship of UMass Amherst and other organization. The determination will drive the type of legal agreement required to formally establish the relationship.  This is a significant decision because it determines the allocation of responsibilities and the appropriate application of indirect cost rates. In the case of a subcontract, it is incumbent upon our University to ensure that subcontractors conduct their portions of research projects in compliance with all applicable terms and conditions of awards and that project costs incurred by subcontractors are reasonable and allowable. Agreements with vendors for the purchase of services (“fee for service”), however, typically do not bind vendors to the full set of NIH terms and conditions.

Some of the terminology that you may be using in certain contexts may have very specific definitions for NIH and the University. For example, while the NIH defines a consultant as an individual who provides professional advice or services for a fee, a consultant is not directly responsible for the completion of the project’s “aims” and does not conduct research but rather acts in an advisory role lending only their expertise. For more information, see “Proposal Preparation Guide: Consultant”.  

A subcontract is a formal legal agreement between our University and another organization. This agreement is used when a substantive portion of the work outlined in a proposal is conducted at another organization. Commonly, the other organization is another educational or research institution, but can be any organization outside the University. Click here for a list of the documentation needed to initiate a subcontract.

If the individual or company in question provides a service for which an established published flat fee is routinely charged for the work to be done and they are not involved in the research effort per se but simply provide a fee for service, this transaction is classified as a standard procurement rather than a subcontract. As such, no statement of work, budget, or letter of intent is needed. Provide OPAS with a copy of the published rate sheet for these services.

Lastly, NIH defines individuals who commit to contribute to the scientific development or execution of the project, but do not commit any specified measurable effort to the project as Other Significant Contributors (OSC), these individuals may even be UMass Amherst faculty or staff. OSCs are typically presented at effort of “zero person months” in the Personnel Justification if modular, or the Budget Justification if non-modular.  OSCs are usually respected, established faculty (external or internal) who may provide the PI or other key personnel guidance on an as needed basis.

If you have any doubt as to participant roles in your proposed sponsored project please do not hesitate to consult an OPAS representative to flesh out the specifics and make a determination as to appropriate roles. (Top)


Know your limits. Carefully read the Funding Opportunity Announcement for budget criteria. You should look for limits on the types of expenses (e.g. no construction allowed), spending caps on certain expenses (e.g. travel limited to $10,000), and overall funding limits (e.g. total costs cannot exceed $300,000 per year, etc.).

NIH uses two different formats for budget submission depending on the total direct costs requested and the activity code used. The SF424 (R&R) Application Guide includes two optional budget components—(1) R&R Budget Component requesting detailed budget information; and, (2) the “simplified” PHS398 Modular Budget Component. Note: NIH applications will include either the R&R Budget Component or the PHS398 Modular Budget Component, but not both. NIH provides the following useful flowchart to determine what budget type to use:


For more information on other considerations to take into account when developing NIH budgets please click here (link is external).


Modular Budget Process


The modular research grant application format is an extension of NIH's streamlining and reinvention initiatives, designed to focus the attention of investigators, their institutions, peer reviewers, and NIH staff on science rather than budget details.


Unless otherwise stated in the guidelines (PA, RFP, or RFA)*, the modular budget process is in effect for the following grant mechanisms at the following levels:

*(Program Announcement, Request for Proposal, Request for Application)

  Grant type

Annual modular max

(direct costs)

Award project period

& total direct cost maximum allowed



5 year limit



2 year limit – must be modular



2 year limit; total limit = $275K



3 year limit; total limit = $250K; budget all direct costs to Year 1



3 years limit; total limit = $450K



2 year limit; total limit -= $450K


For a modular budget proposal, investigators do not have to submit a detailed budget with categorical budget line items to the NIH.  Instead, proposing institutions submit a Modular budget with annual total direct costs built using $25,000 increments up to the maximum annual amount and total amount allowed by funding mechanism as noted above.

At UMass Amherst, an internal budget supporting and explaining the modular budget to be  submitted to the NIH need only provide details on the following categories of cost:

  • Personnel
  • Fringe
  • Consultant
  • Equipment
  • Tuition
  • Subcontracts
  • Indirect costs

These seven categories of costs must be budgeted following standard budgeting principles for those categories, but at proposal stage, all other costs can be budgeted in one lump sum without further explanation/justification or breakout in “Other Direct Costs.”

Investigators (or their business support experts) do not need to provide an internal budget justification for the above seven categories of cost if sufficient details are provided in the Kuali record or Excel budget (if the Kuali budget feature is not utilized).

Just-In-Time (JIT) stage

If the proposal scores well enough to result in a Just-In-Time request from the NIH, the “Other Direct Costs” budgeted in a lump sum must be broken out into individual budget categories (Materials/supplies, Facilities, Animal Care costs, etc.).  To enable JIT review, investigators (or their business support experts) must provide a detailed justification via email to the assigned Pre-award Administrator – see Proposal Staff Contacts.  Any realignment of costs at this stage should not affect the level of effort for personnel, or impact the ratio of direct and indirect costs.  The JIT budget explanation for “Other Direct Costs” should be presented in a tabular format with a detailed narrative of each cost provided as well.

Important considerations

  • Subcontractor (consortium) Facilities & Administrative (i.e., indirect) costs are not included in the modular direct cost limits.  Another way to put this:  the direct cost budget can exceed the annual modular cost caps by the amount of subcontractor overhead budgeted per year.
  • Subcontractors must provide UMass with detailed annual budgets approved by  authorizing officials of the institution.

What budget related documents get loaded to the proposal?

  • Personnel Justification” – this will reflect the personnel budgeted and further explained in the internal budget;  investigators should follow the NIH formatting requirements.  The level of effort in person months must equal the amount budgeted in the internal budget.  This document gets loaded into the PHS 398 Modular Budget Form
  • Proposals that include subcontracts must include a “Consortium Justification” for the subcontractor(s) – see link as above.  While a detailed budget justification is needed from each subcontractor for internal purposes, the “Consortium Justification” reflects the role and level of effort in the subcontractor budget & justification.  This document gets loaded to the PHS Modular Budget Form
  • While the NIH does not require a detailed budget, it is still recommended that investigators utilizing the Modular Budget process build their own internal budgets, since building out the “other direct costs” will help confirm the investigator’s ability to conduct the project for the funds budgeted. 
  • Unless the investigator opts to have the Pre-award team vet that internal budget fully at initial proposal submission, the full budget details (inclusive of details on “Other Direct Costs”) should be held in abeyance by the investigator and submitted to the Pre-award Administrator only when the proposal is selected for JIT review.  This should make for a more efficient process since not all proposals get invited for the JIT process.



NIH Salary Cap

The NIH has historically restricted the amount of direct salary an individual may charge an NIH grant or contract. Commonly referred as the “NIH salary cap, ” it has, for a number of years, been  linked to the Executive Level II salaries of the federal executive pay scale and adjusted whenever federal salaries were increased. The Consolidated Appropriations Act, 2021, Public Law 116-260, Division H, Section 202, restricts the amount of direct salary which may be paid to an individual under an HHS grant, cooperative agreement, or applicable contract to a rate no greater than Executive Level II of the Executive Schedule Pay TableEffective January 1, 2023, the salary limitation for Executive Level II is $212,100. See the Fact Sheet for the current rate.

NIH Salary Cap Example Calculations

Assume PI Smith earns $162,000 for a nine-month academic appointment. Smith’s monthly salary is $18,000 ($162,000/9 months) and annualized salary is $216,000 ($18,000 x 12) which is above the NIH annual salary cap of $203,700 and must be cost shared by the University. Furthermore, assume Smith is committing one month of budgeted effort to an NIH grant. The effective NIH salary monthly cap rate is $16,975 ($203,700/12), and the difference between the monthly capped rate ($16,975) and the monthly UMass rate ($18,000) equals $1,025. This amount above the cap must be funded by non-federal sources and shown as cost-share in the institutional commitments section of Kuali. See the relevant quick guide for more information.   (Top)

Graduate Student Compensation on NIH Grants

Compensation for graduate students on NIH grants includes salary/wages, fringe benefits, and tuition. NIH has established the zero-level postdoctoral NRSA stipend as the benchmark for an award amount that approximates a reasonable rate of compensation for graduate students. The maximum compensation (salary & fringe & tuition) for graduate students should not exceed the zero-level National Research Service Award (NRSA) stipend in effect at the time of the award.

 NIH’s zero-level postdoctoral NRSA stipend is $53,760 as of January 27, 2021. Under no circumstances should a graduate student appointed to an NIH grant be compensated in an amount that exceeds $53,760 inclusive of fringe benefits and tuition.

For the NIH policy, see NIH Graduate Student Compensation (Notice NOT-OD-02-017). For the latest NRSA stipend levels, see NIH Ruth L. Kirschstein National Research Service Award (NRSA).

Research Performance Progress Report (RPPR)

When NIH funds your proposal, NIH will require an annual Progress Report to document your accomplishments and compliance with the terms of award. NIH requires that Progress Reports be submitted by an Authorized Organization Representative therefore, the Progress Report has to be submitted through OPAS by the “Signing Official.”

The Research Performance Progress Report (RPPR) is required for all awards issued under the Streamlined Non-competing Award Process (SNAP), and all F awards, with budget start dates on or after July 1, 2013. NIH continues development of the RPPR for non-SNAP awards, including complex and training awards, and will update the community as progress is made in that regard (see the table below to determine if your award requires RPPR submission).



Streamlined Non-Competing Award Process (SNAP)

RPPR – required


RPPR – required


RPPR – required

Multi-Year-Funded (MYF)

RPPR – required

Phase I Final Year
(Phase II Type 4 Application)

PHS 398 or PHS 2590 - defined by terms of award

RPPR and the NIH Public Access Policy

The NIH public access policy applies to any manuscript thatis: (1) peer-reviewed, (2) accepted for publication in a journal on or after April 7, 2008, and, (3) arises from any direct funding from an NIH grant or cooperative agreement active in Fiscal Year 2008 or beyond. This policy requires that manuscripts resulting from NIH funding be linked with the PubMed Central archive. PIs will need to use the bibliography tool My NCBI (link is external)to link papers to their Progress Reports. The RPPR process allows the NIH to screen for compliance with the NIH public access policy. Publications and manuscripts listed and subject to NIH Public Access policy must include the PubMed Central reference number. NIH will not award non-competing continuation awards when the RPPR publications are not in compliance with the Public Access Policy.

Please note that NIH is increasingly focusing on the Public Access policy at the time of submission of grant proposals as well.  When preparing your submission documents ensure that the Selected Peer-Reviewed Publications section of your NIH biosketch is also compliant with the Public Access policy. (Top)

Change of Institution applications - transfer grant process

Below are the instructions for completing an NIH grant transfer from your current institution to your new institution.  You will have to coordinate the relinquishing date from the originating awardee institution and the start date of the grant at the new institution. 

If transferring out of UMass, you must follow the steps as outlined on the Transfer of Grants. page and then also follow the instructions below.  Coordination with the Controller’s Office is needed for the generation of the relinquishing statement.  

If you are transferring to UMass from another institution, it is important that prior to your appointment, the department or college business manager work with you to gain access to electronic systems needed to process your transfer request (scroll to criteria #3; Non-Employees or Pending Employees). The business manager in the department or at the college level will guide you through the University proposal process, assist with development of the transfer request, and develop the budget according to the University requirements for NIH funding.

Questions on the transfer process can be directed to the NIH proposal staff contact at OPAS.

From the Current Grantee Institution

Official Statement Relinquishing Interests and Rights in a PHS Research Grant is submitted via electronic Research Administration Commons (eRA Commons).  The transfer application cannot be processed until this form has been submitted.  This form provides the effective date of relinquishment, estimated unexpended Direct and Facilities and Administrative (F&A) Costs (funds from previous budget periods should not be included in these amounts), and a list of equipment costing $5,000 or more transferring with the project. 

Relinquishing Statement Resources:

Form HHS 568, Final Invention Statement and Certification. While this form is not required until 90 days after the project terminates, it is desirable to submit it with the transfer request documents.

Standard Form 425, Financial Status Report (FFR).  The FFR must be submitted by the original awardee institution within 90 days following termination of the project. 

Unobligated funds must be reflected as carryover in the required carryover field of the FSR in order for the funds to be available to the PI for expenditure at the new institution.  These funds will be issued to the new institution after the change of institution application is submitted and awarded by the NIH. (Top)

From the Proposed New Institution                                                              

Contact the NIH Grants Management Specialist (GMS) assigned to the existing award in order to confirm the next steps, although generally they will not diverge from the steps noted below:

The proposed new institution should begin preparing its transfer application (detailed below) to submit as soon as possible (prior to the date on the relinquishing statement). This is especially true if the grantee is planning to transfer to an organization that has not previously received NIH support—the transfer will take longer to complete once it is approved because the proposed organization will need an established EIN and possibly an FWA, animal assurance, and IRB or IACUC approvals.  The University of Massachusetts Amherst has a current EIN and FWA registration, but accommodations should be made for IRB/IACUC review and approval as applicable.

For instructions on how to complete an electronic change of institution application, please visit the NIH Parent Announcement website and scroll to the bottom of the webpage for “Change of Grantee Organization (Type 7 Parent Clinical Trial Optional)” – currently this is PA-18-590. 

Be sure to always follow the instructions provided by the NIH Grants Management Specialist (GMS) if they diverge from the NIH Parent Announcement for Change of Grantee Organization applications.

UMass Specific:  for change of institution applications being submitted by UMass on behalf of incoming faculty, the proposal should be built in the University’s electronic proposal administration system using the Program Announcement noted above. 

The electronic application from the proposed grantee institution should include, at a minimum, the following information: 

  • SF 424 (R&R) Cover Page

Field 4.a. (Federal Identifier) populate with the institute and serial number of the grant (e.g. CA987654)

Field 8 (Type of Application), select “Revision” and then mark “E. Other” and insert “Change of Grantee Organization” in the text field

  • PHS 398 Cover Page Supplement

Complete applicable fields

  • SF 424 (R&R) Other Project information

Human Subjects section:  Provide the Office for Human Research Protections (OHRP) assurance number and IRB approval for the new organization, if applicable

Vertebrate Animals section:  Provide the Office of Laboratory Animal Welfare (OLAW) assurance number and IACUC approval for the new organization, if applicable

Facilities & other Resources: Include probable effect of the move on the project

Equipment:  Include detailed list of any equipment purchased with grant funds to be transferred to the new organization (inclusion of this list in the transfer application from the new organization indicates its acceptance of title to that equipment);

  • SF 424 (R&R) Project/Performance Site Location(s)
  • SF 424 Research & Related Senior/Key Person Profile:

Updated biographical sketches for the PD/PI and existing senior/key personnel and biographical sketches for any proposed new senior/key personnel, and updated "Other Support" page(s) as necessary – if there are changes since last reporting.

  • R&R Budget Form

The R&R Detailed Budget form must be used, regardless of the form used for the initial application for current award for all research and career mechanisms.

The budget should be based on the direct costs relinquished by the original grantee organization, unless otherwise instructed by the awarding IC.  On top of that, budget the F&A costs at the new institution’s rates.  The budget is not typically constrained by the amount of F&A awarded originally.

Even if the budget for the original award was submitted in a modular format, the R&R Detailed Budget form must be used for an electronic application for change of grantee organization. For these modular budget based awards, grantees may either complete all of the fields in the R&R Detailed Budget as appropriate or, they may complete only the costs for the PD/PI (Section A), and include the remainder of the direct costs under Section F (Other Direct Costs) Item 8, and Section H (Indirect Costs).

UMass Specific:  If a detailed budget is not provided due to it being modular, a detailed budget must be routed with the other materials for internal review purposes.

Cost of Living Adjustments (COLA).  It is advisable for change of institution applications to forgo using COLAs since in the past when utilized, the NIH will sometimes opt for level funding salaries & fringe, but keep all other direct costs as proposed if cuts were built in at budgeting stage to accommodate increases to labor.

  • PHS Research Plan Form

Include a statement indicating whether the overall research plans/aims have changed from the original submission. If the overall research plans/aims have changed, provide updated information.

If the overall research plans/aims have not changed, load the original research plans/aims to the change of institution proposal.

If transferring on the anniversary date, include the progress report for the current year that includes a statement regarding the goals for the upcoming year.

If transferring during the budget period (i.e., a mid-year transfer), contact the awarding IC to determine if a progress report is required. If required, the progress report should be included in the Research Strategy section. 

UMass specific:  if the research plans/aims do not change as a result of the change of institutions, provide a copy of the Specific Aims and Research Strategy from the original awarded proposal.  Please route along with the other materials. This is for internal purposes only.

Other considerations for faculty transferring to UMass

Affiliation of Commons ID to UMass needed.  Contact the OPAS Pre-award team member handling the NIH portfolio. (Top)

Effort Reporting

As previously mentioned, NIH requires progress reports to be submitted via an Authorized Organization Representative (OPAS); therefore, the University must make a reasonable attempt to vet the information contained in the progress report. One of the trickiest aspects of the progress report process is effort reporting. University faculty and staff are expected to charge their time to sponsored awards commensurate with the committed effort expended on all activities they perform. Payroll charges to sponsored awards, serve as the initial data points for the University’s effort reporting system. OMB A-21 states, “In the use of any methods for apportioning salaries, it is recognized that, in an academic setting, teaching, research, service, and administration are often inextricably intermingled. A precise assessment of factors that contribute to costs is not always feasible, nor is it expected. Reliance, therefore, is placed on estimates in which a degree of tolerance is appropriate.” The effort certification should be a reasonable estimate of how time was expended but there must be correspondence between the effort expected by the NIH as submitted in the proposal and the amount charged to the grant. Simply put, effort reported must equal effort charged to the grant. It is the policy of the University to assume a cost-sharing commitment only when required by the sponsor or by the competitive nature of the award, and then to cost share only to the extent necessary to meet the specific requirements (Please review the Unified Policy and Procedure Guide to Cost Sharing).

At the time of preparing the progress report, it is important to be in contact with the necessary administrative support who can help you verify the official effort that has been devoted to the sponsored project in question.

Please review this important guidance on Effort Commitments. (Top)

NIH Financial Conflict of Interest Requirements

The U.S. Public Health Service (PHS) amended its Financial Conflict of Interest (FCOI) Regulations effective August 24, 2012. These regulations have unique reporting and conflict management requirements and require an initial disclosure of all financial interest related to the institutional responsibilities of the investigator to the UMass Amherst Office of Research Compliance.

Faculty investigators who are supported by U.S. Public Health Service (PHS) funding, including, but not limited to, NIH, CDC, HRSA, SAMHSA, FDA, and AHRQ, are required to submit a PHS Conflict of Interest Disclosure Form to the UMass Office of Research Compliance at the point of each proposal submission and receive training on the regulations.

Other Resources