First Interlaboratory Comparison Exercise for Lipidomics Collection

NIST Generic Clearance for Program Evaluation Data Collections

0693-0033-FirstInterLaboratoryComparison-Lipidomics-CollectionInstrument-ScreenShots-3-13-17

First Interlaboratory Comparison Exercise for Lipidomics Collection

OMB: 0693-0033

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Basic Information

OMB Control #0693-0033
Expiration Date: 06/30/2019
1. Name of participant (optional):

* 2. Title/Position

* 3. Number of people in laboratory
5 or under

5 to 10

10 to 15

over 15

* 4. Type of institution (select those that apply)
Academia

Core Facility

Industry

Government

5. Laboratory PI name (if same as above, fill in see above)

* 6. Name of Institution

* 7. Location

Other

About the Laboratory

OMB Control #0693-0033
Expiration Date: 06/30/2019
* 8. How long has your laboratory been performing lipidomics?
< 1 year
1 to 5 years
5 to 10 years
> 10 years

* 9. Approximately how many lipid samples does your laboratory analyze in a month?
< 50
50 to 100
100 to 500
> 500

* 10. Approximately how many lipidomics manuscripts does your laboratory publish per year?
0
1 to 3
3 to 5
>5

* 11. What kind of lipid applications do you typically work on in your laboratory (select those that apply)?
Clinical and medical science

Toxicology

Environmental science

Biomarker discovery

Food science

Plant science

Drug development/discovery

Forensics

Natural products

Other (please specify)

* 12. What kind of sample matrices does your laboratory analyze for lipidomics (select those that apply)?
plasma

saliva/sweat/tears

serum

dried blood spots

urine

breast milk

tissues

food

cells

plant materials

feces
Other (please specify)

* 13. What strategies (if any) does your laboratory employ for enhancing/monitoring lipid stability (select
those that apply)?
antioxidant addition

sample preparation performed on ice

use of inhibitors

use of heat treatment

use of internal/recovery standards

derivatization

flash freezing

no specific strategies employed

Other (please specify)

* 14. What kind of separation technique does your laboratory use in tandem with mass spectrometry for
lipidomics (select those that apply)?
ion mobility

high performance liquid
chromatography

shotgun/direct infusion

direct analysis (ex., DART, DESI)
gas chromatography

ultra-high performance liquid
chromatography
Other (please specify)

15. If chromatography, what type of column(s) does your laboratory use for lipidomics?

* 16. What kind of instruments does your laboratory use for the above mentioned methods (select those that
apply)?
Orbitrap

Fourier Transform Ion Cyclotron
Resonance

Flame Ionization Detector

Quadrupole Time-of-Flight
Ion Trap
Triple Quadrupole
Nuclear Magnetic Resonance
Other (please specify)

* 17. What data acquisition methods does your laboratory incorporate for targeted studies (select those that
apply)?
neutral loss scans

single/selected reaction monitoring

parent ion scans

we only apply untargeted approaches

product ion scans
Other (please specify)

* 18. What data acquisition methods does your laboratory incorporate for untargeted studies (select those
that apply)?
accurate mass

data independent MS/MS

data dependent low-resolution MS/MS

we only employ targeted approaches

data dependent high-resolution MS/MS
Other (please specify)

* 19. If you incorporate a high-resolution mass spectrometer, at what mass resolving power do you analyze
your lipid extracts (answer N/A if you only use a low-resolution mass spectrometer)?

* 20. What lipid categories do you routinely measure in your laboratory (select those that apply)?
Fatty Acyl Lipids

Sphingolipids

Saccharolipids

Glycerolipids

Sterol Lipids

Polyketides

Glycerophospholipids

Prenol Lipids

Other (please specify)

* 21. For untargeted lipidomics experiments, what lipid extraction does your laboratory employ (select those
that apply)?
Bligh-Dyer

MTBE (Matyash)

Solid Phase Extraction

Folch

Supercritical Fluid Extraction

We do not perform untargeted
lipidomics experiments

Other (please specify)

* 22. If you use LC-MS, what software does your laboratory employ for peak picking/processing (select all
that apply)?
Manual (Xcalibur, MassHunter,
MassLynx, other)

MS-DIAL

Progenesis QI

Lipidyzer

Compound Discoverer

SimLipid

We do not use LC-MS

MZmine
XCMS
Sieve
LipidSearch
Other (please specify)

* 23. What software does your laboratory employ for lipid identification (select all that apply)?
Manual (visual inspection)

MS-LAMP

Greazy

LipidSearch

LIMSA

LipidBlast

Lipidyzer

LOBSTAHS

LipidPioneer

SimLipid

Lipid Data Analyzer

mzCloud

Alex

LipidQA

LipidMatch

LipidXplorer

Lipid-Pro

Other (please specify)

* 24. What lipid databases do you use (select those that apply)?
Japan’s LipidBank

LipidHome

LIPID MAPS

Cyberlipid

LipidBlast

SphinGOMAP

European Lipidomics Initiative

mzCloud

SwissLipids

NIST Mass Spectrometry Database

Other (please specify)

* 25. What software does your laboratory employ for lipid quantification (select those that apply)?
Manual

Sieve

LipidSearch

TraceFinder

Lipidyzer

Progenesis QI

SimLipid
Other (please specify)

* 26. What software does your laboratory employ for lipid quality control and statistics (select those that
apply)?
MetaboAnalyst

Orange

S-PLUS

SPSS

JMP

NCSS

Excel

Tableau

GraphPad Prism

R-tools

TraceFinder

Statistica

PLS_Toolbox

MATLAB

PSPP

Origin

Stata

Analyze-it

Galaxy toolbox

Minitab

SYSTAT

Other (please specify)

Lipid Quantitation

OMB Control #0693-0033
Expiration Date: 06/30/2019
* 27. What type of quantitation do you perform in your laboratory?
absolute

relative

semi-quant

not interested in quantitation of lipids

* 28. Is absolute quantitation something that could be important to your laboratory?
Yes
No

* 29. On average, how many lipid internal standards do you use per lipid class?
1

2

3 or more

* 30. What type of internal standards does your laboratory most often employ (select those that apply)?
odd-chain

deuterated

low fatty acyl carbon chain (12:0 or
less)

carbon-13 labeled

Isotopic Ratio Outlier Analysis

Other (please specify)

* 31. Do you make your own lipid internal standard mix or buy pre-made mixtures?
We make our own internal standard mixtures
We buy pre-made internal standard mixtures
We do both

* 32. What lipids do you find most challenging to quantitate (select those that apply)?
free/total fatty acids

sphingomyelins

phosphatidylethanolamines

cholesterol

eicosanoids

phosphatidylglycerols

cholesteryl esters

bile acids

phosphatidylinositols

triacylglycerols

lysophosphatidylcholines

phosphatidylserines

diacylglycerols

lysophosphatidylethanolamines

phosphatidic acids

ceramides

phosphatidylcholines

Other (please specify)

* 33. Does your laboratory employ relative response factors (RRFs) for these lipid categories (select those
that apply)?
Fatty acyl
lipids

Glycerolipids

Glycerophos
pholipids

Sphingolipids

Sterols

All of the
above

We do not
employ RRFs
Other (please specify)

* 34. How does your laboratory treat multiple adducts per lipid (select those that apply)?
sum them

use the most intense for each ionization
mode

average them
report individual adducts (no further
processing)
Other (please specify)

* 35. When processing lipid data, does your laboratory use peak height or peak area for quantitation?
peak height
peak area

* 36. How does your laboratory normalize your quantitative lipid values (select those that apply)?
total protein

dry weight

normalize by sum of feature values

DNA

wet weight

probabilistic quotient normalization

cell count

TIC

no normalization

Other (please specify)

Reference Material/Quality Control

OMB Control #0693-0033
Expiration Date: 06/30/2019
* 37. Do you have written standard operating procedures (SOPs) in your laboratory, and if so, what aspects
do the SOPs cover (select those that apply)?
instrument calibration/maintenance

data processing

sample collection

monitoring lipid stability

sample extraction

assessment of data quality/quality control

sample storage

we do not have SOPs in our laboratory

instrument operation
Other (please specify)

* 38. Has your laboratory adopted the proposed shorthand annotation style for lipid structures at the fatty
acyl level (doi:10.1194/jlr.M033506), when the sn1 and sn2 position of the fatty acyl chains is unknown
(e.g., PC 16:0_18:1)?
Yes
No

* 39. What types of quality control (QC) samples does your laboratory use in analytical measurements for
lipidomics?
no QC materials

pooled samples (matrix-matched)

solvent blanks

pooled samples (not matrix-matched)

extraction blanks

NIST Standard Reference Materials
(SRMs)

Certified Reference Materials (CRMs)

Other (please specify)

40. For question 35, state whether the QC material you employ is commercially available or made in-house.
For commercially available answers, please specify the material name.

* 41. What does your laboratory use QCs, SRMs, or CRMs for (select those that apply)?
Establishing metrological traceability

Method validation (method variance)

Technical variance

Calibration

Establish trueness of result

We don't use QCs, SRMs, or CRMs

Value assignment of secondary reference material
Other (please specify)

* 42. If your laboratory uses commercially available QC materials (ex. NIST SRMs), please indicate below;
however, if your laboratory does not use commercially available reference materials, indicate why below?
we use commercially
available QCs

don't know about
them

don’t see value

too expensive

correct matrix not
available
Other (please specify)

* 43. What type of reference material would be of most interest to your laboratory?
Complex biological matrix

Lipid internal standard mixture

Lipid standard mixture

Spiked standards in a complex biological matrix

* 44. What types of complex biological reference materials would you like to see provided?
plasma

cells

breast milk

serum

feces

food

urine

saliva/sweat/tears

plant materials

tissues

dried blood spots

not interested in reference materials

Other (please specify)

* 45. Do you validate your project sample measurements with:
repeated extractions of a sample (with analysis)

reviewing measurements of a previously described quality
control sample run in the same batch

repeated instrument analysis of a sample
test set
sent to outside laboratory
no validation process employed
use a complimentary approach to confirm
Other (please specify)

* 46. About how long does your laboratory store extracted lipidomics samples before you discard?
Less than a day

One month to less than 6 months

One day to less than a week

6 months to a year

One week to less than a month

Greater than a year

47. What temperature(s) does your laboratory store lipid extracts at (select those that apply)?
room temperature

freezer (-80 C)

refrigerated (2-4 C)

liquid nitrogen

freezer (-20 C)
Other (please specify)

* 48. Does your laboratory store your lipid data in a repository? If yes, where?

Other Questions

OMB Control #0693-0033
Expiration Date: 06/30/2019
* 49. What do you perceive as the biggest challenge in the lipidomics community (select those that apply)?
lack of standardization of methods/protocols within the
community

quantitation
over reporting/false positives

lack of standards
lack of lipid centric training/workshops
software/data handling
lipid annotation
Other (please specify)

* 50. Has your laboratory ever participated in an interlaboratory comparison study or ring trial?
Yes
No

* 51. Would your laboratory be interested in participating in a future NIST interlaboratory study?
Yes
No

* 52. Do you feel there are enough opportunities and/or lipidomics conferences per year to present lipidomics
studies?
Yes
No

* 53. Would you be interested in attending or presenting at a Gordon Research Conference focused on the
measurement science of lipidomics and metabolomics?
Attending
Presenting
No interest

54. Additional comments?

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National Institute of Standards and Technology, Attn: John A. Bowden (john.bowden@nist.gov).

OMB Control No. 0693-0033
Expiration Date: 06/30/2019


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