using these databases on datasets generated using a different
chromatographic separation, annotations of MS signals must
be confirmed by MS/MS experiments. The time saved using
database for the annotation of large MS datasets is to the user’s
appreciation.
18. When comparing the lipid profile of different strains, it is
desirable to ensure that the cultures are in the same growth
phase (log versus late phase). One replicate culture in the
presence of detergent can be carried out in parallel with
detergent-free cultures for each strain, in order to estimate
their growth phase based on optical density measurement.
References
1. Jurowski K, Kochan K, Walczak J, Baranska M,
Piekoszewski W, Buszewski B (2017) Analytical techniques in Lipidomics: state of the art.
Crit Rev Anal Chem 47(5):418–437. https://
doi.org/10.1080/10408347.2017.1310613
2. Zullig T, Trotzmuller M, Kofeler HC (2020)
Lipidomics from sample preparation to data
analysis: a primer. Anal Bioanal Chem 412
(10):2191–2209. https://doi.org/10.1007/
s00216-019-02241-y
3. Minnikin DE, Brennan PJ (2020) Lipids of
clinically significant mycobacteria. In: Goldfine
H (ed) Health Consequences of Microbial
Interactions with Hydrocarbons, Oils, and
Lipids. Handbook of Hydrocarbon and Lipid
Microbiology. Springer, Cham, pp 1–76.
https://doi.org/10.1007/978-3-319-724737_7-1
4. Becker K, Sander P (2016) Mycobacterium
tuberculosis lipoproteins in virulence and
immunity—fighting with a double-edged
sword. FEBS Lett 590(21):3800–3819.
https://doi.org/10.1002/1873-3468.12273
5. Neyrolles O, Guilhot C (2011) Recent
advances in deciphering the contribution of
Mycobacterium tuberculosis lipids to pathogenesis. Tuberculosis 91(3):187–195. https://doi.
org/10.1016/j.tube.2011.01.002
6. Ray A, Cot M, Puzo G, Gilleron M, Nigou J
(2013) Bacterial cell wall macroamphiphiles:
pathogenÀ/microbe-associated molecular patterns detected by mammalian innate immune
system. Biochimie 95(1):33–42. https://doi.
org/10.1016/j.biochi.2012.06.007
7. Chiaradia L, Lefebvre C, Parra J, Marcoux J,
Burlet-Schiltz O, Etienne G, Tropis M, Daffe
M (2017) Dissecting the mycobacterial cell
envelope and defining the composition of the
native mycomembrane. Sci Rep 7(1):12807.
https://doi.org/10.1038/s41598-01712718-4
8. Hoffmann C, Leis A, Niederweis M, Plitzko
JM, Engelhardt H (2008) Disclosure of the
mycobacterial outer membrane: cryo-electron
tomography and vitreous sections reveal the
lipid bilayer structure. Proc Natl Acad Sci U S
A 105(10):3963–3967. https://doi.org/10.
1073/pnas.0709530105
9. Zuber B, Chami M, Houssin C, Dubochet J,
Griffiths G, Daffe M (2008) Direct visualization of the outer membrane of mycobacteria
and corynebacteria in their native state. J Bacteriol 190(16):5672–5680. https://doi.org/
10.1128/JB.01919-07
10. Bansal-Mutalik R, Nikaido H (2014) Mycobacterial outer membrane is a lipid bilayer and
the inner membrane is unusually rich in diacyl
phosphatidylinositol dimannosides. Proc Natl
Acad Sci U S A 111(13):4958–4963. https://
doi.org/10.1073/pnas.1403078111
11. Sani M, Houben EN, Geurtsen J, Pierson J, de
Punder K, van Zon M, Wever B, Piersma SR,
Jimenez CR, Daffe M, Appelmelk BJ, Bitter W,
van der Wel N, Peters PJ (2010) Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1secreted proteins. PLoS Pathog 6(3):
e1000794. https://doi.org/10.1371/journal.
ppat.1000794
12. Layre E, Sweet L, Hong S, Madigan CA,
Desjardins D, Young DC, Cheng TY, Annand
JW, Kim K, Shamputa IC, McConnell MJ,
Debono CA, Behar SM, Minnaard AJ,
Murray M, Barry CE 3rd, Matsunaga I,
Moody DB (2011) A comparative lipidomics
platform for chemotaxonomic analysis of Mycobacterium tuberculosis. Chem Biol 18
(12):1537–1549. https://doi.org/10.1016/j.
chembiol.2011.10.013
13. Becker K, Haldimann K, Selchow P, Reinau
LM, Dal Molin M, Sander P (2017) Lipoprotein glycosylation by protein-O-Mannosyltransferase (MAB_1122c) contributes to low
Targeted Lipidomics
575
chromatographic separation, annotations of MS signals must
be confirmed by MS/MS experiments. The time saved using
database for the annotation of large MS datasets is to the user’s
appreciation.
18. When comparing the lipid profile of different strains, it is
desirable to ensure that the cultures are in the same growth
phase (log versus late phase). One replicate culture in the
presence of detergent can be carried out in parallel with
detergent-free cultures for each strain, in order to estimate
their growth phase based on optical density measurement.
References
1. Jurowski K, Kochan K, Walczak J, Baranska M,
Piekoszewski W, Buszewski B (2017) Analytical techniques in Lipidomics: state of the art.
Crit Rev Anal Chem 47(5):418–437. https://
doi.org/10.1080/10408347.2017.1310613
2. Zullig T, Trotzmuller M, Kofeler HC (2020)
Lipidomics from sample preparation to data
analysis: a primer. Anal Bioanal Chem 412
(10):2191–2209. https://doi.org/10.1007/
s00216-019-02241-y
3. Minnikin DE, Brennan PJ (2020) Lipids of
clinically significant mycobacteria. In: Goldfine
H (ed) Health Consequences of Microbial
Interactions with Hydrocarbons, Oils, and
Lipids. Handbook of Hydrocarbon and Lipid
Microbiology. Springer, Cham, pp 1–76.
https://doi.org/10.1007/978-3-319-724737_7-1
4. Becker K, Sander P (2016) Mycobacterium
tuberculosis lipoproteins in virulence and
immunity—fighting with a double-edged
sword. FEBS Lett 590(21):3800–3819.
https://doi.org/10.1002/1873-3468.12273
5. Neyrolles O, Guilhot C (2011) Recent
advances in deciphering the contribution of
Mycobacterium tuberculosis lipids to pathogenesis. Tuberculosis 91(3):187–195. https://doi.
org/10.1016/j.tube.2011.01.002
6. Ray A, Cot M, Puzo G, Gilleron M, Nigou J
(2013) Bacterial cell wall macroamphiphiles:
pathogenÀ/microbe-associated molecular patterns detected by mammalian innate immune
system. Biochimie 95(1):33–42. https://doi.
org/10.1016/j.biochi.2012.06.007
7. Chiaradia L, Lefebvre C, Parra J, Marcoux J,
Burlet-Schiltz O, Etienne G, Tropis M, Daffe
M (2017) Dissecting the mycobacterial cell
envelope and defining the composition of the
native mycomembrane. Sci Rep 7(1):12807.
https://doi.org/10.1038/s41598-01712718-4
8. Hoffmann C, Leis A, Niederweis M, Plitzko
JM, Engelhardt H (2008) Disclosure of the
mycobacterial outer membrane: cryo-electron
tomography and vitreous sections reveal the
lipid bilayer structure. Proc Natl Acad Sci U S
A 105(10):3963–3967. https://doi.org/10.
1073/pnas.0709530105
9. Zuber B, Chami M, Houssin C, Dubochet J,
Griffiths G, Daffe M (2008) Direct visualization of the outer membrane of mycobacteria
and corynebacteria in their native state. J Bacteriol 190(16):5672–5680. https://doi.org/
10.1128/JB.01919-07
10. Bansal-Mutalik R, Nikaido H (2014) Mycobacterial outer membrane is a lipid bilayer and
the inner membrane is unusually rich in diacyl
phosphatidylinositol dimannosides. Proc Natl
Acad Sci U S A 111(13):4958–4963. https://
doi.org/10.1073/pnas.1403078111
11. Sani M, Houben EN, Geurtsen J, Pierson J, de
Punder K, van Zon M, Wever B, Piersma SR,
Jimenez CR, Daffe M, Appelmelk BJ, Bitter W,
van der Wel N, Peters PJ (2010) Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1secreted proteins. PLoS Pathog 6(3):
e1000794. https://doi.org/10.1371/journal.
ppat.1000794
12. Layre E, Sweet L, Hong S, Madigan CA,
Desjardins D, Young DC, Cheng TY, Annand
JW, Kim K, Shamputa IC, McConnell MJ,
Debono CA, Behar SM, Minnaard AJ,
Murray M, Barry CE 3rd, Matsunaga I,
Moody DB (2011) A comparative lipidomics
platform for chemotaxonomic analysis of Mycobacterium tuberculosis. Chem Biol 18
(12):1537–1549. https://doi.org/10.1016/j.
chembiol.2011.10.013
13. Becker K, Haldimann K, Selchow P, Reinau
LM, Dal Molin M, Sander P (2017) Lipoprotein glycosylation by protein-O-Mannosyltransferase (MAB_1122c) contributes to low
Targeted Lipidomics
575