Projects/MIAPE:Summary list

a) Global descriptors   Date stamp (as YYYY-MM-DD) Responsible person (or institutional role if more appropriate); provide name, affiliation and stable contact information Instrument manufacturer and model Customisations (summary)

b) Control and analysis software   Software name and version Switching criteria (tandem only) Isolation width (global, or by MS level) Location of ‘parameters’ file

a) Electrospray Ionisation (ESI)   Supply type (static, or fed) Interface manufacturer, model and catalog number (where available) Sprayer type, coating, manufacturer, model and catalogue number (where available) Relevant voltages where appropriate (tip, cone, acceleration) Other parameters if discriminant for the experiment (such as nebulising gas and pressure)

b) MALDI   Plate composition (or type) Matrix composition (if applicable) Deposition technique Relevant voltages where appropriate (Grid, acceleration) PSD (or LID/ISD) summary, if performed Operation with or without delayed extraction Laser type (e.g., nitrogen) and wavelength (nm) Other laser related parameters, if discriminating for the experiment (such as pulse energy (µJ), attenuation, focus diameter (µm), pulse duration (ns at FWHM), frequency (Hz) and average shots fired per spectrum)

a) Ion optics, ‘simple’ quadrupoles, hexapoles   No parameters to be captured

b) Time-of-flight drift tube (TOF)   Reflectron status (on, off, none)

c) Ion trap   Final MS stage achieved

d) Collision cell   Gas type and pressure (bar) Collision energy

e) FT-ICR   As for ‘Ion trap’ (3c) and ‘Collision cell’ (3d) combined, no further parameters required

f) Detectors   Detector type Detector sensitivity

a) Spectrum description   Location of source (‘raw’) file including file name and type Identifying information for the target area (MALDI-like methods only) MS level for this spectrum Ion mode for this spectrum Precursor m/z and charge, with the full mass spectrum containing that peak (for MS level 2 and higher)

b) Peak list generation   Parameters triggering the generation of peak lists from raw data, including filtering for exclusion of peak lists from raw spectra, where appropriate Acquisition number (from the ‘raw’ file) of all acquisitions combined in the peak list, the total number combined and whether summed or averaged Smoothing; whether applied, parameters Background threshold, or algorithm used Signal-to-noise estimation and method Percentage peak height for centroiding; or algorithm used, if appropriate Whether charge states were calculated, spectra were deconvoluted and peaks were deisotoped (with methods described as appropriate) Relative times for all acquisitions combined in the peak list (electrospray only) Base peak m/z, where appropriate Metastable peaks removed, if applicable m/z and intensity values

c) Quantitation for selected ions (in addition to 4a and 4b)   Only applicable if a quantitation experiment has been performed   Experimental protocol, canonical reference where available with deviations Number of combined samples and MS runs analysed Quantitation approach (e.g., integration) Normalisation technique Location of quantitation data, with file name and type (where appropriate)

a) Global descriptors   Date stamp (as YYYY-MM-DD) Responsible person (or institutional role if more appropriate); provide name, affiliation and stable contact information Software name, version and manufacturer Customisations made to that software Availability of that software Location of the files generated; parameter files, spectral data (input/output)

a) Input data   Description and type of MS data Availability of MS data (source of data, file format)

b) Input parameters   Databases queried; description and versions (including number of entries searched) Taxonomical restrictions applied Description of tool and scoring scheme Specified cleavage agent(s) Allowed number of missed cleavages Additional parameters related to cleavage Permissible amino acids modifications Precursor-ion and fragment ion mass tolerance for tandem MS (when applicable) Mass tolerance for PMF (when applicable) Thresholds; minimum scores for peptides, proteins (probabilities, number of hits, other metrics) Any other relevant parameters

a) For identified proteins   Accession code in the queried database Protein description Protein scores Validation status Number of different peptide sequences (without considering modifications) assigned to the protein Percent peptide coverage of protein Identity of supporting peptides In the case of PMF, number of matched/unmatched peaks

b) For identified peptides   Sequence (indicate any deviation from the expected protein cleavage specificity) Peptide scores Chemical modifications (artefactual) and post-translational modifications (naturally occurring); sequence polymorphisms with experimental evidence (particularly for isobaric modifications) Corresponding spectrum locus Charge assumed for identification and a measurement of peptide mass error Other additional information, when used for evaluation of confidence

c) Quantitation for selected ions   Quantitation approach (e.g. 4plex-iTRAQ, ICAT, cICAT, COFRADIC) Quantity measurement (e.g. integration of signals, use of signal intensity) Data transformation and normalisation technique (description of method and software) Number of replicates (biological and technical) Acceptance criteria (including measure of errors) Estimates of uncertainty and the methods for the error analysis, including the treatment of relevant systematic error effects and the treatment of random error issues Results from controls (when described)

Location of source (‘raw’) file including file name and type Identifying information for the target area (MALDI-like methods only) MS level for this spectrum

1.1.1 Date stamp (as yyyy-mm-dd) 1.1.2 Responsible person or institutional role 1.1.3 Electrophoresis type

2.1.1 Sample name(s) 2.1.2 Loading buffer

3.1. Dimension details   3.1.1 Ordinal number for this dimension 3.1.2 Separation method employed

3.2 Gel matrix   3.2.1 Description of gel matrix 3.2.2 Gel manufacturer 3.2.3 Physical dimensions 3.2.4 The physicochemical property range and distribution (as appropriate) 3.2.5 Acrylamide concentration 3.2.6 Acrylamide : Crosslinker ratio 3.2.7 Additional substances in gel 3.2.8 Gel lane 3.2.9 Sample application

3.3 Protocol   3.3.1 Buffers 3.3.2 Electrophoresis conditions

4.1 Inter-dimension process   4.1.1 Step name 4.1.2 Inter-Dimension buffer 4.1.3 Additional reagents 4.1.4 Equipment 4.1.5 Protocol

5.1 Direct detection   5.1.1 Name of direct detection process 5.1.2 Direct detection agents 5.1.3 Additional reagents and buffers 5.1.4 Equipment 5.1.5 Direct detection protocol

5.2 Indirect detection   5.2.1 Name of indirect detection process 5.2.2 Transfer medium 5.2.3 Detection medium 5.2.4 Indirect detection agents 5.2.5 Additional reagents and buffers 5.2.6 Equipment 5.2.7 Indirect detection protocol

6.1 Acquisition equipment   6.1.1 Type of equipment 6.1.2 Name of equipment 6.1.3 Software 6.1.4 Calibration (if appropriate) 6.1.5 Equipment specific parameters

6.2 Acquisition protocol   6.2.1 Image acquisition process 6.2.2 Reference to gel matrix

7.1.1 Image name (or id) 7.1.2 Dimensions 7.1.3 Resolution 7.1.4 Bit depth 7.1.5 Image location 7.1.6 Standard image orientation