DOI: 10.5281/zenodo.14929539
title: Raw data for the Manuscript "A glycosylated lipooctapeptide promotes uptake and growth of Mycobacterium abscessus in the host", by Leclercq and collaborator, Nature Communication 2025

description: This dataset contains raw data from liquid NMR and MALDI TOF experiments that were used to establish the fine structure of a newly discovered glycopeptidolipids extracted from the pathogenic bacteria Mycobacterium abscessus.

NMR spectra of the 1H and 13C nuclei were acquired at 293K using cryo-TCI or TBI probes and AVANCE Neo consoles (BRUKER BIOSPIN GmbH, Rheinstetten, Germany), with resonance frequencies of 1H at 400 - 900 - 1200 MHz. Standard pulse sequences recommended by the manufacturer (zg; selcssfdizs.2; cosygpqf; dipsi2etgpsi; noesygpph; hsqcedetgpsisp2.2; hsqcdietgpsisp2; hmbcetgpl3nd) were used for each homonuclear (1H/1H COSY = COrrelation SpectroscopY highlights vicinal protons; 1H/1H TOCSY = TOtal Correlation SpectroscopY; 1H/1H NOESY = Nuclear Overhauser Effect SpectroscopY highlights spatial proximity of protons less than 5-6 Angström) or heteronuclear experiment (1H/13C HSQC = Heteronuclear Single Quantum Coherence shows proton linked to their carbon; 1H/13C HMBC = Heteronuclear Multiple Bond Correlation highlights quaternary carbon not linked to proton). After acquisition, spectra underwent phase correction and referencing to the residual methanol signal (δ 1H/δ 13C = 3.31/49.29 ppm). Data were analysed with Topspin 4.0.6.

MALDI data was acquired on a Axima Resonance (SHIMADZU, Kyoto, Japan). Laser energy was optimized for each sample between 90 eV and 130 eV, and acquisition was conducted in positive reflectron mode, from 50 Da to 3000 Da mass range. External calibration was performed on glucidex polysaccharides covering the same mass range. For MS2and MS3 analyses, the parent ions were selected with a resolution of 250 and 70 then collided with a voltage between 300 V and 600 V.

High-field Fourier transform Ion Cyclotron Resonance (FT-ICR) MS was carried out on SolariX MRMS (BRUKER DALTONICS GmbH, Bremen, Germany), equipped with a 12 T superconducting magnet and a dynamically harmonized ICR cell, in positive ion mode. Before spotting, one volume of sample, one volume of PEG2000 (1 mM in water) as an internal standard, and two volumes of matrix were mixed. The laser was set to 25% of power, and the mass range was selected from 150 to 3000 Da. 10-20 scans, each resulting from 200 laser shots, were accumulated for each mass spectra, which were recorded using 4 million points (transient 1.12 s).

Raw data are connected to Figures and Supplementary figures in the manuscript as described below:



Figure 3d MALDI – MALDI-MS spectra of polar lipids from Mabs R WT, D4690c, D4690c::4690c strains

Figure 4a NMR - 1H/1H TOCSY and 1H/1H NOESY NMR spectra of GL8Pb acquired in CDCl3/CD3OH (2:1) at 293K

Figure 4e NMR - 1H/1H COSY and 1H/1H NOESY NMR spectra of LGL8Pb

Figure 5a MALDI - MS2 and MS3 fragmentation of the parent ion at m/z 1750 GL8Pb generated [M-88+Na]+ fragment at m/z 1662

Figure 5b MALDI - MS2 and MS3 fragmentation of the parent ion at m/z 1392 GL8Pa produced [M-88+Na]+ fragment at m/z 1304

Figure 5 FT-ICR - FT-ICR analysis of GL8Pa and GL8Pb

Figure S1b MALDI – MALDI-MS analysis of Ac1PIM2 purified from M. abscessus R polar lipids

Figure S1c MALDI – MALDI-MS2 analysis of Ac1PIM2 purified from M. abscessus R polar lipids

Figure S1d MALDI - MALDI-MS spectra in positive mode of polar lipids from R, R△MAB_4690c::4690c and R△4690c 

Figure S2a MALDI - MALDI-TOF MS analysis of fraction 17 and fraction 22 of silica gel separation

Figure 2b NMR - 1H/13C HSQC and 1H/1H TOCSY NMR of 3,4 di-O-acyl trehalose

Figure S2c MALDI - MALDI-TOF MSn analysis of 3,4 di-O-acyl trehalose

Figure S2e MALDI - MALDI-TOF MS analysis of fraction 61 and fraction 64 of reverse-phase liquid chromatography separation

Figure S3a NMR - 1H/13C HSQC NMR spectra of purified GL8Pb acquired in CDCl3/CD3OD (2:1)

Figure S3b NMR - 1H/1H COSY NMR spectra of purified GL8Pb acquired in CDCl3/CD3OD (2:1)

Figure S4 COSY NMR - 1H/1H COSY NMR spectra of purified GL8Pb

Figure S4 NOESY NMR - 1H/1H NOESY NMR spectra of purified GL8Pb

Figure S4/S5 HSQC NMR - 1H/13C HSQC NMR spectra of purified GL8Pb

Figure S4/S5 HMBC NMR - 1H/13C HMBC NMR spectra of purified GL8Pb

Figure S6c MALDI - MS2 and MS3 fragmentation of the parent ion at m/z 1778 generated [M-88+Na]+ fragment at m/z 1690.

Figure S7a MALDI - MALDI-MS spectra in positive mode of polar lipids from R, R△4690c (red) and R△MAB_4691c.