Mass spectrometry informatics

From MIBBI

1. General features

1.1. Global descriptors

1.1.1. Date

1.1.2. Person or responsible role

1.1.3. Software name, version and manufacturer

1.1.4. Customisations made to that software

1.1.5. Availability of that software

1.1.6. Location of the files generated¹

2. Input data and parameters

2.1. Input data

2.1.1. Description and type of MS data

2.1.2. Availability of MS data²

2.2. Input parameters

2.2.1. Databases queried³

2.2.2. Taxonomical restrictions applied

2.2.3. Description of tool and scoring scheme

2.2.4. Specified cleavage agent or agents

2.2.5. Allowed number of missed cleavages

2.2.6. Additional parameters related to cleavage

2.2.7. Permissible amino acids modifications

2.2.8. Precursor-ion and fragment ion mass tolerance for tandem MS⁴

2.2.9. Mass tolerance for PMF⁵

2.2.10. Thresholds - minimum scores for peptides and proteins⁶

2.2.11. Any other relevant parameters

3. The output from the procedure⁷

3.1. For identified proteins

3.1.1. Accession code in the queried database

3.1.2. Protein description

3.1.3. Protein scores

3.1.4. Validation status

3.1.5. Number of different peptide sequences assigned to the protein⁸

3.1.6. Percent peptide coverage of protein

3.1.7. Identity of supporting peptides

3.1.8. Number of matched and unmatched peaks⁹

3.2. For identified peptides

3.2.1. Sequence¹⁰

3.2.2. Peptide scores

3.2.3. Occurrence and position of amino acid modifications¹¹

3.2.4. Corresponding spectrum locus

3.2.5. Charge assumed for identification and a measurement of peptide mass error

3.2.6. Other additional information when used for evaluation of confidence

3.3. Quantitation for selected ions

3.3.1. Quantitation approach

3.3.2. Quantity measurement

3.3.3. Data transformation and normalisation technique¹²

3.3.4. Number of replicates¹³

3.3.5. Acceptance criteria¹⁴

3.3.6. Estimates of uncertainty and the methods for the error analysis¹⁵

4. Interpretation and validation

4.1. Assessment and confidence given to the identification and quantitation¹⁶

4.2. Results of statistical analysis¹⁷

4.3. Inclusion/exclusion of the output of the software¹⁸

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Footnotes

¹ Parameter files, spectral data (input/output).

² Source of data, file format.

³ Description and versions (including number of entries searched).

⁴ If applicable.

⁵ If applicable.

⁶ Probabilities, number of hits, other metrics.

⁷ The procedure might generate all or part of the elements described below (identified proteins, identified peptides, quantization information). Select the elements that apply.

⁸ Without considering modifications.

⁹ Applicable to PMF only.

¹⁰ Indicate any deviation from the expected protein cleavage specificity.

¹¹ These should be reported as artefactual (such as oxidized Met or Carbamidomethylated Cys), post-translational (such as myristoylated amino acid), issued from an amino acid mutation or a frame shift with respect to the sequence in the database. When a choice among possible isobaric modifications are reported, a justification should be applied (I/L, acetylation/trimethylation).

¹² Description of method and software.

¹³ Both biological and technical.

¹⁴ Include measure of errors.

¹⁵ Includes the treatment of relevant systematic error effects and the treatment of random error issues.

¹⁶ Description of methods, thresholds, values, etc.

¹⁷ Or determination of false positive rate in case of large scale experiments.

¹⁸ Description of what part of the output has been kept, what part has been rejected.

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Sources

MIAPE

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Notes

This module identifies the minimum information required to report the use of protein and peptide identification and characterisation software to analyse the data produced by mass spectrometry experiments, sufficient to support both the effective interpretation and assessment of the data and the potential recreation of the work that generated it.