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1. What are the MCP publication guidelines?
2. Do I need to deposit my raw mass spectrometry data?
3. What are the acceptable repositories to deposit my mass spectrometry data?
4. What are annotated spectra?
5. Do I need to provide annotated spectra?
6. How do I provide annotated spectra that support the assignments reported in my manuscript?
7. Do I need to complete the mass spectrometry checklists for the publication guidelines during the submission process?
8. Does my manuscript require a paragraph titled "Experimental Design and Statistical Rationale"?
9. Is my manuscript checked for compliance to the guidelines?

1. What are the MCP publication guidelines?

   The MCP publication guidelines describe the information required by the journal for all articles dealing with mass spectrometric analyses designed for protein, peptide or posttranslational modification (PTM) identification and their quantification, regardless of whether the study is biological or clinical in focus. This information is deemed the minimum information required in order for a reviewer/reader to be able to assess the reliability of published results. The guidelines can be found here. We have also provided a tutorial to assist authors to comply with these guidelines and explain the reasoning behind them. MCP also has separate targeted mass spectrometry guidelines for manuscripts that describe measurements of peptides, modified peptides and proteins using targeted MS approaches (MRM, PRM), clinical guidelines for manuscripts containing data obtained from human subjects, guidelines for glycomic studies for manuscripts reporting identification of free or released glycans, glycopeptides or glycolipids, and data-independent acquisition (DIA) guidelines for studies employing DIA strategies. All manuscripts are checked for compliance to these guidelines in parallel with the review process.

2. Do I need to deposit my raw mass spectrometry data?

   Yes. We require that all raw mass spectrometric output files in the original instrument vendor file format be deposited in a publicly accessible repository at the time of submission. Many of these repositories allow for password-protected submissions that only become public upon acceptance of the manuscript. Authors need to provide the appropriate information describing the data deposit, including the location of the repository and identifying information (URL, project ID) in the manuscript under a subsection titled "Data Availability" after the Acknowledgments, and the login details for reviewers' purposes in the cover letter.

3. What are the acceptable repositories to deposit my mass spectrometry data?

   We require that mass spectrometry data be deposited in a publicly accessible repository that is independent of the authors' control. MCP does not officially endorse any one repository. However, repositories that are part of the ProteomeXchange Consortium are suitable choices. These include the PRIDE Archive, MassIVE, jPOST and iProX, and for targeted proteomics data, PeptideAtlas and Panorama Public . Other acceptable public repositories include, but are not limited to, Chorus. Since repositories need to be beyond author's control, lab websites or personal repositories (e.g., Dropbox, Google Drive) are thus not acceptable. Data deposits on lab or university websites in addition to the publicly accessible repositories are however acceptable to the journal.

4. What are annotated spectra?

   Annotated spectra are experimentally determined tandem mass spectra that establish the particular amino acid sequence and any covalent modification site(s) present. These spectra must be labeled with both the m/z values for all significant peaks in the spectra, as well as their fragment ion designations (e.g., y, b, etc. if spectra are from an MS/MS experiment) supporting the sequence being reported.

5. Do I need to provide annotated spectra?

   The current MCP guidelines require that annotated spectra be provided in these instances: (1) proteins identified on the basis of the sequence of a single unique peptide (multiple identifications of the same peptide is a single unique peptide), and (2) post-translationally modified (PTM) peptide/protein site assignments. Please note that these spectral requirements for covalent PTMs do not extend to peptides containing oxidized methionine or other chemical modifications introduced for quantification or stabilization.

6. How do I provide annotated spectra that support the assignments reported in my manuscript?

   Annotated spectra can be provided in the text as necessary, and as supplementary material with the article. However, when files are large (>100 MB) e.g. as may be the case in studies involving large-scale identifications of PTMs, storage in a publicly accessible repository is acceptable. MCP has provided a guide to help authors in providing annotated spectra through deposition in public repositories.

7. Do I need to complete the mass spectrometry checklists for the publication guidelines during the submission process?

   While we no longer require authors to complete the checklists during the submission process, authors should review all guidelines and their checklists prior to submission to ensure that all required information and data are provided. Failure to provide the relevant information as required by the guidelines might prevent or delay the review process. On the submission form, authors need to choose which guidelines are pertinent to their manuscript and provide the reviewer’s login information to access the raw data deposit.

8. Does my manuscript require a paragraph titled "Experimental Design and Statistical Rationale"?

   For manuscripts containing mass spectrometry identifications, we require a separate paragraph under the Experimental Procedures section that contains details about numbers of replicates, whether they are biological or technical repeats, and justification for why this experimental design has sufficient statistical power to support the biological claims and conclusions. Refer to the authors' checklist for the items that need to be included in this paragraph. Obviously, not all of these items are necessarily relevant to your manuscript. The goal of having this paragraph is to make the experimental design of the mass spectrometry experiments performed clear and easy to understand and can be duplicated by others.

9. Is my manuscript checked for compliance to the guidelines?

   Yes, your manuscript will be checked for compliance to the relevant guidelines during the peer review process. If there are missing items or compliance issues, these will be noted in the editor's decision letter. Authors need to resolve all compliance issues prior to resubmitting, as manuscripts will not be accepted until all compliance issues have been resolved.

Please feel free to contact [email protected] with any questions about MCP.