NIST lipidomics workflow questionnaire: an assessment of community-wide methodologies and perspectives

Abstract

Introduction: Efforts to harmonize lipidomic methodologies have been limited within the community. Here, we aimed to capitalize on the recent National Institute of Standards and Technology lipidomics interlaboratory comparison exercise by implementing a questionnaire that assessed current methodologies, quantitation strategies, standard operating procedures (SOPs), and quality control activities employed by the lipidomics community.

Objectives: Lipidomics is a rapidly developing field with diverse applications. At present, there are no community-vetted methods to assess measurement comparability or data quality. Thus, a major impetus of this questionnaire was to profile current efforts, highlight areas of need, and establish future objectives in an effort to harmonize lipidomics workflows.

Methods: The 54-question survey inquired about laboratory demographics, lipidomic methodologies and SOPs, analytical platforms, quantitation, reference materials, quality control procedures, and opinions regarding challenges existing within the community.

Results: A total of 125 laboratories participated in the questionnaire. A broad overview of results highlighted a wide methodological diversity within current lipidomic workflows. The impact of this diversity on lipid measurement and quantitation is currently unknown and needs to be explored further. While some laboratories do incorporate SOPs and quality control activities, these concepts have not been fully embraced by the community. The top five perceived challenges within the lipidomics community were a lack of standardization amongst methods/protocols, lack of lipid standards, software/data handling and quantification, and over-reporting/false positives.

Conclusion: The questionnaire provided an overview of current lipidomics methodologies and further promoted the need for community-accepted guidelines and protocols. The questionnaire also served as a platform to help determine and prioritize metrological issues to be investigated.

Keywords: Harmonization; Lipidomics; Methodology; Quality Control; Quantitation; Questionnaire.

Fig. 1

“What lipid categories do you routinely measure in your laboratory (select those that apply)?” The values are shown as a percentage of total responses (total number of laboratories responding, n = 125). The overall total number of responses was 542. The number of responses are indicated in the figure above the solid bars. The x axis labels reflect the survey multiple choice response options. Note that for this question, laboratories had the option to self-identify with more than one option

Fig. 2

“What kind of sample matrices does your laboratory analyze for lipidomics (select those that apply)”. The values are shown as a percentage of total responses (total number of laboratories responding, n = 125). The overall total number of responses was 633. The number of responses are indicated in the figure above the solid bars. The x axis labels reflect the survey multiple choice response options. Note that for this question, laboratories had the option to self-identify with more than one option. The write-in responses included bronchoalveolar lavage, cerebrospinal fluid (CSF), yeast, microbes, meibum, and model organisms

Fig. 3

“What strategies (if any) does your laboratory employ for enhancing/monitoring lipid stability (select those that apply)?” The values are shown as a percentage of total responses (total number of laboratories responding, n = 125). The overall total number of responses was 353. The number of responses are indicated in the figure above the solid bars. The x axis labels reflect the survey multiple choice response options. Note that for this question, laboratories had the option to self-identify with more than one option

Fig. 4

“What kind of separation technique does your laboratory use in tandem with mass spectrometry for lipidomics (select those that apply)?” The values are shown as a percentage of total responses (total number of laboratories responding, n = 125). The overall total number of responses was 319. The number of responses are indicated in the figure above the solid bars. The x axis labels reflect the survey multiple choice response options. Note that for this question, laboratories had the option to self-identify with more than one option. Write-in responses included thin-layer chromatography, matrix assisted laser desorption/ionization (MALDI), and imaging

Fig. 5

“What kind of instruments does your laboratory use for the methods mentioned in Fig. 4 (select those that apply)?” The values are shown as a percentage of total responses (total number of laboratories responding, n = 125). The overall total number of responses was 263. The number of responses are indicated in the figure above the solid bars. The x axis labels reflect the survey multiple choice response options. Note that for this question, laboratories had the option to self-identify with more than one option. Write-in responses included quadrupole and Triple TOF

Fig. 6

“What data acquisition methods does your laboratory incorporate for targeted studies (select those that apply)?” The values are shown as a percentage of total responses (total number of laboratories responding, n = 125). The overall total number of responses was 316. The number of responses are indicated in the figure above the solid bars. The x axis labels reflect the survey multiple choice response options. Note that for this question, laboratories had the option to self-identify with more than one option

Fig. 7

“What data acquisition methods does your laboratory incorporate for untargeted studies (select those that apply)?” The values are shown as a percentage of total responses (total number of laboratories responding, n = 125). The overall total number of responses was 316. The number of responses are indicated in the figure above the solid bars. The x axis labels reflect the survey multiple choice response options. Note that for this question, laboratories had the option to self-identify with more than one option