workflow – lipidomicstandards.org

Title of the study *

Type of workflow *

Type of workflow

Targeted / Untargeted *

Is the workflow targeted or untargeted?

Quantative *

Is the workflow quantitative, i.e. concentrations are reported?

Clinical *

Is it clinical lipidomics, i.e. samples were analyzed related to a clinical question using a quantitative, validated method?

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Table of preanalytical details *

Details of the sample preanalytics are reported in a separate table.

Table of preanalytical details *

Click or drag a file to this area to upload.

Upload table in the defined format

Sample type(s) *

Plasma
Serum
Cells
Tissue
Other solid material
Urine
Feces
Other non-solid material

Specify the type(s) of the sample material(s)

Perfusion *

Was blood removed from the organ(s) by perfusion?

Time to separate plasma/serum (min)

Time from drawing the sample until centrifugation.

Temp handling original sample *

Temperature until freezing or extraction.

Preparation fresh *

Lipid extraction was performed instantely after sample collection?

Time to freeze (min) *

Time until freezing of sample.

Snap freezing in liquid N2 *

Was liquid nitrogen used for initial freezing?

Storage temp *

Temperature the samples stored until sample preperation.

Storage time (month) *

Time of sample storage until lipid extraction

Freeze-thaw cycles *

How many freeze-thaw cycles underwent the sample?

Additives *

BHT
lipase inhibitors
other

Were the samples stored with additional preservenats or in buffers/solvents?

Other additives *

Which other additives were used?

Intert gas *

Were samples stored under inert gas?

Biobank samples *

Were the samples received from a biobank?

One pot homogenization and extraction

Was the sample homogenized and extracted in one step?

Homogenization

Was the sample homogenized prior lipid extraction?

Homogenization solvent

PBS
saline
water
methanol
other solvent

Which solvent was used for homogenization?

Other homogenization solvent *

Which other homogenization solvent(s) was/were used?

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Extraction method *

Which type of lipid extraction was applied?

Other extraction method *

Which other extraction method was applied?

pH adjustment *

Was the pH adjusted for extraction? If yes, which buffer, acid/base was added?

1-phase system *

Type of 1-phase, i.e. organic solvent used for protein precipitation.

2-phase system *

Type of 2-phase; for other include reference when available.

Solid-Phase Extraction *

Separation mode applied for SPE.

Internal standards added *

Were internal standards added prior extraction?

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MS type *

QqQ
QTOF
Orbitrap
ICR
other

Which instrument type was applied?

Other MS type *

Specify another MS type.

MS vendor *

Thermo
Agilent
SCIEX
Waters
Shimadzu
Bruker
other

Vendor of mass spectrometer.

Other MS vendor *

Specify another MS vendor.

Ion source *

ESI
APCI
APPI
MALDI
other

Which ion source was applied?

Other ion source *

Specify another ion source.

Imaging ion source

Which ion source was applied?

Other imaging ion source *

Specify another imaging ion source.

Separation

Was a separation method applied?

Direct-Type *

Syringe
FIA
Chip

Which inlet was used for direct MS?

Additional dimension/techniques *

Were additional analytical dimensions applied?

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Additional table *

Details for individal lipid classes were included in a separate table

File Upload *

Click or drag a file to this area to upload.

An exemplary table template can be downloaded here.

MS level *

Which MS level(s) was(were) used for identification?

Mass resolution for detected ion *

Which mass resolution was applied for the detected ion?

Mass accuracy window *

Maximal mass deviation for identification (±)

Mass window for precursor selection *

For MS2 and higher - which mass window (±) was applied for precursor selection?

Polarity *

positive
negative

Which polarity was applied for analysis?

Isotope correction @ MS1 *

Was Type II overlap corrected?

Isotope correction @ MSn *

Was Type II overlap corrected?

MS1 verified by standard *

Were standards used to check which precursor ions are formed for the lipid class?

MSn verified by standard *

Were standards used to check which fragment ions are formed for the lipid class?

Background check @ MS1 *

Was checked whether background ions interfere ?

Background check @ MSn *

Was checked whether background ions interfere ?

Check isomer overlap *

Was interference by isomeric lipid classes excluded (see LSI table)?

Check isobar overlap *

Was interference by isobaric lipid classes excluded (see LSI table)?

Check in-source fragmentation *

Was interference by in-source fragmentation excluded (see LSI table)?

Lipid Identification Software *

Which software was applied for lipid identification

Signal to noise *

Was a signal to noise ratio >3 applied?

Data manipulation *

Smoothing
Centroiding
Look Mass Correction
background correction
none

Nomenclature for intact lipid molecule *

Was the latest shorthand notation (doi: 10.1194/jlr.S120001025) used for annotation?

Nomenclature for fragment ions *

Was the recommended annotation of fragment ions (doi: 10.1371/journal.pone.0188394 ) applied?

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Additional table *

Details for individual lipid classes were included in a separate table

File Upload *

Click or drag a file to this area to upload.

An exemplary table template can be downloaded here.

Number of separation dimensions

How many separation dimensions were applied?

Separation type

Which type of separation was applied?

Separation mode

NP
HILIC
RP
other

Which separation mode was applied?

Other separation mode *

Which other separation mode was applied?

RT verified by standard

Were standards used to check retention time of lipid class(species)?

Model for separation prediction

Was a model used to predict lipid molecule separation?

Separation of isobaric/isomeric interferece confirmed

Was separation of isobaric/isomeric interference confirmed by analytical standards?

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Additional table *

Details for individual lipid classes were included in a separate table

File Upload *

Click or drag a file to this area to upload.

An exemplary table template can be downloaded here.

Number of additional dimension/techniques

How many additional analyctic dimensions applied?

Additional dimension/techniques

Were additional analytic dimensions applied?

Other additional dimension/techniques *

Which other dimension or technique was applied?

CCS verified by standard *

Were standards used to check CCS values?

Separation of isobaric/isomeric interferece confirmed *

Was separation of isobaric/isomeric interferece confirmed by analytical standards?

Model for separation prediction *

Was a model used to predict lipid molecule separation?

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Additional table

Details for individual lipid classes were included in a separate table

File Upload *

Click or drag a file to this area to upload.

An exemplary table template can be downloaded here.

Internal lipid standard(s)

Were lipid class specific internal standards used?

Internal lipid standard species

Which internal standard(s) was(were) used for quantification?

Type of quantification

How were the samples quantified?

Type of calibration line

Which type of calibration was used?

Species calibration line

Which lipid molecules were used for calibration

Response correction

Was the analytical response corrected?

Type I isotope correction

Was isotopic abundance of individual species corrected (Type I)?

Normalization

Which reference was used for normalization?

Other normalization *

Which other normalization was applied?

Unit

Unit of the reported data?

Other unit *

Which other unit was used?

Lipid Quantification Software

Software used for quantification

Batch correction

Was a batch correction applied?

Other batch correction

Which other batch correction was applied?

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Blanks *

Where blank samples analyzed?

Type of Blanks *

Which types of blank samples were analyzed?

Quality control *

Were QC samples analyzed?

Type of QC sample *

Pooled plasma
commercial sample
sample pool
reference material

Which types of QC samples were analyzed?

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Dynamic quantification range

Limit of quantitation (LOQ)/Limit of detection (LOD)

Precison

Accuracy

Guidelines followed

Other guidelines followed *

Which other guidelines were followed?

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Data upload *

Were reported data uploaded into repository or included as supplementary data?

Metadata

Are metadata available?

Summary data

Quantification data
Identification data
both

Are summary, i.e. processed final data available?

Raw data upload

Are raw data, i.e. unprocessed data including peak m/z, intensities/areas, RT (when applicable) available?