Publication Guidelines for the Analysis and Documentation of Peptide and Protein Identifications - include key method details

Sep 21, 2026

Uploaded by Terk

Publication guidelines describing what supporting information to include when reporting peptide and protein identifications from mass spectrometry. The document specifies required details for peak-list generation, database searching (programs, versions, parameters, sequence sources, search sizes), MS/MS interpretation confidence criteria, and statistical validation such as false-positive estimation for large-scale studies. It also lists required reporting fields per identified protein sequence and per peptide, plus expectations for quantitative proteomics validation and post-translational modification site evidence.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages4

Reading Time10 min

AccessFree to download

Supporting information for manuscripts

Peak list generation and database search details

MS/MS interpretation thresholds and statistical validation

Reporting requirements by identified protein and peptide

Protein-level fields

Peptide-level fields for single-peptide identifications

Additional potentially valuable information

Quantitative proteomics: experimental design and validation

Biological and analytical reliability validation

Systematic and random error handling

Uncertainty and error analysis reporting

Post-translational modifications: specialized evidence

Publication Guidelines for the Analysis and Documentation of Peptide and Protein Identifications 1. The following supporting information should be included with the manuscript: • The method and/or program (including version number) used to create the “peak list” from the raw data and the parameters used in the creation of this peak list, particularly any which might affect the quality of the subsequent database search. Examples include whether smoothing was applied, any signal-to-noise criteria, whether charge states were calculated or peaks de-isotoped, etc. In cases where additional customized processing of the collections of peak lists has been performed, e.g. clustering or filtering, the method and/or program (including version number) should be referenced. • The name and version of the program(s) used for database searching and the values of search parameters. Examples include precursor-ion mass tolerance, fragment-ion mass tolerance, modifications allowed for, any missed cleavages, protein cleavage chemistry ,(if any), etc. • The name and version of the sequence database(s) used. If a database was compiled in-house, a complete description of the source of the sequences is required. The number of entries actually searched from each database should be included. Authors should justify the use of a very small database or database that excludes common contaminants, since this may generate misleading assignments. • Methods used to interpret MS/MS data, thresholds and values specific to judging certainty of identification, whether any statistical analysis was applied to validate the results, and a description of how applied. • For large-scale experiments, provide the results of any additional statistical analyses that indicate or establish a measure of identification certainty, or allow a determination of the false-positive rate, e.g., the results of randomized database searches or other computational approaches. 2. Information for each protein sequence identified should specify the following: • accession number and database source; • score(s) and any associated statistical information obtained for searches conducted; • sequence coverage, expressed as the number of amino acids spanned by the assigned peptides divided by the sequence length; • the total number ofpeptides assigned to the protein. To compute this number, multiple matches to peptides with the same primary sequence count as one, even if they represent different charge states or modification states; In addition to the above information, for single peptide-based identifications the following data should be provided: • peptide sequence, noting any deviation from the expected protein cleavage specificity; • modifications; • precursor mass, charge and mass error observed; • score(s) and any associated statistical information; • MS/MS spectrum annotated with masses observed as well as fragment assignments 3. Additional potentially valuable information could include the retention time of each peptide, the observation of multiple charge states, multiple observations of the same peptide, flanking residues, start and end positions of peptides in proteins, and any platform-specific information. 4. Manuscripts presenting any conclusions citing quantitative proteomic results should contain the following information: The experimental design and data analysis methods should be described in sufficient detail to enable critical assessment of the reliability of the results and conclusions. All relevant quantitative data must be made available. The amount of data and method description is considered sufficient when it is possible to reproduce the reported results or critically reanalyze the data. Citation of standard methods covered in publications or specialized software may be used. However, where any deviations exist and for all methods not covered by citation, authors must describe: • The methods for how the biological reliability of measu

FAQs

What supporting details must be included for generating the peak list from raw data?

Include the method and/or program used to create the peak list and the parameters that could affect database search quality, such as smoothing, signal-to-noise criteria, charge-state calculation, or peak de-isotoping. If customized processing like clustering or filtering was performed, reference the method and program (including version).

What information is required for each identified protein sequence?

Report the accession number and database source; the score(s) and any associated statistical information from searches; sequence coverage (amino acids spanned divided by sequence length); and the total number of assigned peptides. For single-peptide identifications, provide peptide sequence (noting cleavage specificity deviations), modifications, precursor mass/charge/mass error, score(s) and statistics, and an annotated MS/MS spectrum with observed masses and fragment assignments.

How should quantitative proteomic results be validated and reported?

Describe experimental design and data analysis methods in sufficient detail to enable critical assessment and reproduction or reanalysis. Explain how biological reliability was validated (e.g., biological replicates, statistical methods, independent experiments), and how analytical reliability was validated (e.g., technical replicates, statistical methods). Address systematic and random errors, provide uncertainty estimates for all quantitative results used for conclusions, and clearly describe error-analysis methods; insufficient validation including error analysis can lead to rejection.

Sep 21, 2026

Uploaded by Terk