Mass spectrometry

From MIBBI

1. General features

1.1. Global descriptors

1.1.1. Date

1.1.2. Person or responsible role

1.1.3. Instrument manufacturer and model

1.1.4. Customisations¹

1.2. Control and analysis software

1.2.1. Software name and version

1.2.2. Switching criteria²

1.2.3. Isolation width³

1.2.4. Location of parameters file

2. Ion sources⁴

2.1. Electrospray ionisation

2.1.1. Supply type

2.1.2. Interface manufacturer model and catalog number where available

2.1.3. Sprayer type, coating, manufacturer, model and catalogue number where available

2.1.4. Relevant voltages where appropriate⁵

2.1.5. Other parameters if discriminant for the experiment

2.2. MALDI

2.2.1. Plate composition or type

2.2.2. Matrix composition if applicable

2.2.3. Deposition technique

2.2.4. Relevant voltages where appropriate

2.2.5. PSD summary if performed⁶

2.2.6. Operation with or without delayed extraction

2.2.7. Laser type and wavelength in nm⁷

2.2.8. Other laser related parameters, if discriminating for the experiment

3. Post-source component⁸

3.1. Time-of-flight drift tube

3.1.1. Reflectron status

3.2. Ion trap

3.2.1. Final MS stage achieved

3.3. Collision cell

3.3.1. Gas type and pressure⁹

3.3.2. Collision energy

3.4. Detectors

3.4.1. Detector type

3.4.2. Detector sensitivity

4. Spectrum and peak list generation and annotation¹⁰

4.1. Spectrum description

4.1.1. Location of source file including file name and type¹¹

4.1.2. Identifying information for the target area¹²

4.1.3. MS level for this spectrum

4.1.4. Ion mode for this spectrum

4.1.5. Precursor m/z and charge with the full mass spectrum containing that peak¹³

4.2. Peak list generation

4.2.1. Parameters triggering the generation of peak lists from raw data¹⁴

4.2.2. Acquisition number of all acquisitions combined in the peak list¹⁵

4.2.3. Smoothing¹⁶

4.2.4. Background threshold or algorithm used

4.2.5. Signal-to-noise estimation and method

4.2.6. Percentage peak height for centroiding or algorithm used if appropriate

4.2.7. Whether charge states were calculated, spectra were deconvoluted and peaks were deisotoped¹⁷

4.2.8. Relative times for all acquisitions combined in the peak list¹⁸

4.2.9. Base peak m-to-z where appropriate

4.2.10. Metastable peaks removed if applicable

4.2.11. m-to-z and intensity values

4.3. Quantitation for selected ions¹⁹

4.3.1. Experimental protocol and canonical reference where available with deviations

4.3.2. Number of combined samples and MS runs analysed

4.3.3. Quantitation approach

4.3.4. Normalisation technique

4.3.5. Location of quantitation data with file name and type where appropriate

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Footnotes

¹ Summary thereof.

² Tandem instruments only.

³ Global, or by MS level

⁴ As each spectrum is acquired using only one ionisation source, select only the subcategory that applies.

⁵ Provide tip, cone, acceleration

⁶ Or LID/ISD.

⁷ Nitrogen laser

⁸ As an MS experiment performed on one instrument cannot be acquired using all existing analysers and detectors, select the elements that apply. N.B. Ion optics, ‘simple’ quadrupoles, hexapoles – no parameters to be captured. FT-ICR - As for ‘Ion trap’ and ‘Collision cell’ combined, no further parameters required.

⁹ bar

¹⁰ For this section; if software other than that listed under 'Control and analysis software' is used to perform a task, the producer, name and version of that software must be supplied in each case.

¹¹ The ‘raw’ spectra

¹² MALDI-like methods only.

¹³ For MS level 2 and higher.

¹⁴ Include filtering for exclusion of peak lists from raw spectra, where appropriate.

¹⁵ From the ‘raw’ file - the total number combined and whether summed or averaged

¹⁶ Whether applied, parameters.

¹⁷ With methods described as appropriate.

¹⁸ Electrospray only.

¹⁹ In addition to 'Spectrum description' and 'Peak list generation'. Only applicable if a quantitation experiment has been performed.

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Sources

MIAPE

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Notes

This module identifies the minimum information required to report the use of a mass spectrometer in a proteomics experiment, sufficient to support both the effective interpretation and assessment of the data and the potential recreation of the work that generated it.