(a) Representative peptidoglycan building block made of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) forming a disaccharide subunit linked to a pentapeptide stem attached to the …
The identification of muropeptides was carried out using four successive steps, indicated by different colours (orange, green, blue, and red, respectively). As a first step, observed masses in the …
Breakdown of peptidoglycan is shown by oligomerisation state (left) branching to specific composition (right). Branch size is proportional to percentage. Monomers, dimers, trimers, and glycan chains …
(a) Pearson’s correlation coefficients across biological replicates of R20291 and M7404 C. difficile isolates. Heatmap gradient shows highest value in green to lowest value in red. (b) Muropeptide …
C. difficile mass database.
C. difficile 20291 versus M7404, list of muropeptides, abundance, RT.
(a) Pearson’s correlation coefficients across biological replicates of E. coli BW25113. (b) Muropeptide distribution according to degree of crosslinking. The crosslinking index was calculated as …
Agilent MS data (data: .d) is converted by Proteowizard to a mzML format (data: XML). Relevant settings for Proteowizard are shown (left). mzML file is then converted by TOPPAS to a mzXML file …
mzXML (data: XML) is passed to MaxQuant (process) for deconvolution and monoisotopic mass determination. Default values used except where indicated (right). MaxQuant output (data: text file) is then …
Structure | RT (min) | Abundance (%) | Monoisotopic mass (Da) | |||
---|---|---|---|---|---|---|
Av±SD | Av±SD | Obs | Theo | Δppm | ||
GM|0 | 3.62±0.01 | 3.465±0.683 | 498.205 | 498.206 | 2.5 | |
Glycans | GM (x2)|0 | 10.11±0.03 | 0.428±0.349 | 976.384 | 976.386 | 2.2 |
4.38%±0.35% | GM (anhydro) |0 | 8.20±1.92 | 0.238±0.025 | 478.179 | 478.180 | 2.9 |
GM (deacetyl) |0 | 2.57±0.00 | 0.155±0.032 | 456.194 | 456.196 | 3.5 | |
GM (x2) (deacetyl) |0 | 6.86±0.02 | 0.093±0.012 | 934.372 | 934.376 | 3.2 | |
GM-AEmA|1 | 10.04±0.04 | 36.098±2.131 | 941.405 | 941.408 | 2.8 | |
GM-AEm|1 | 6.57±0.01 | 14.352±0.397 | 870.368 | 870.371 | 3.0 | |
GM-AEmKR|1 | 9.56±0.05 | 8.030±0.774 | 1154.563 | 1154.567 | 3.6 | |
GM-AE|1 | 9.57±0.04 | 1.809±0.231 | 698.284 | 698.286 | 3.1 | |
GM-AEmG|1 | 7.85±0.05 | 0.689±0.049 | 927.390 | 927.392 | 2.3 | |
GM-AEm (anhydro) |1 | 13.98±0.02 | 0.668±0.073 | 850.342 | 850.344 | 2.2 | |
Monomers | GM-AEmA (anhydro) |1 | 16.55±0.01 | 0.573±0.100 | 921.380 | 921.382 | 2.0 |
63.14%±1.13% | GM-AEmAG|1 | 9.45±0.05 | 0.219±0.009 | 998.426 | 998.429 | 3.1 |
GM-AEmKR (anhydro) |1 | 14.83±0.01 | 0.160±0.039 | 1134.537 | 1134.540 | 2.9 | |
GM-AEmA (deacetyl) |1 | 8.57±0.06 | 0.083±0.055 | 899.394 | 899.397 | 3.1 | |
GM-GM-AEmA|1 | 13.10±0.02 | 0.075±0.040 | 1419.584 | 1419.588 | 2.9 | |
GM-AE (anhydro) |1 | 17.44±0.01 | 0.069±0.013 | 678.258 | 678.260 | 2.8 | |
M-AEm|1 | 4.56±0.01 | 0.062±0.064 | 667.289 | 667.291 | 3.8 | |
M-AEmKR|1 | 8.16±0.06 | 0.061±0.056* | 951.484 | 951.487 | 3.2 | |
GM-AEmAA|1 | 11.38±0.04 | 0.059±0.003 | 1012.442 | 1012.445 | 2.4 | |
M-AEmA|1 | 8.52±0.05 | 0.053±0.015 | 738.325 | 738.328 | 4.0 | |
GM-GM-AEm|1 | 11.31±0.04 | 0.042±0.025 | 1348.547 | 1348.551 | 2.4 | |
GM-AEm (deacetyl) |1 | 4.77±0.01 | 0.024±0.014 | 828.358 | 828.360 | 3.0 | |
GM-GM-AEmKR|1 | 12.18±0.03 | 0.011±0.002* | 1632.742 | 1632.747 | 3.0 | |
GM-AEmA-GM-AEmA|2 | 16.01±0.02 | 17.247±0.777 | 1864.800 | 1864.805 | 2.3 | |
GM-AEmA-GM-AEmKR|2 | 14.83±0.02 | 4.589±0.589 | 2077.957 | 2077.964 | 3.0 | |
GM-AEmA-GM-AEm|2 | 15.09±0.02 | 3.207±0.168 | 1793.763 | 1793.768 | 2.6 | |
GM-AEmA-GM-AEmA (anhydro) |2 | 20.56±0.01 | 0.873±0.037 | 1844.774 | 1844.778 | 2.4 | |
GM-AEm-GM-AEmKR|2 | 14.22±0.00 | 0.855±0.101 | 2006.920 | 2006.926 | 3.3 | |
GM-AEmA-GM-AEmKR (anhydro) |2 | 18.89±0.17 | 0.665±0.079 | 2057.934 | 2057.937 | 1.8 | |
GM-AEm-GM-AEm|2 | 14.23±0.01 | 0.558±0.062 | 1722.725 | 1722.730 | 3.0 | |
GM-AEm-GM-AEmAG|2 | 14.68±0.01 | 0.416±0.025 | 1850.785 | 1850.789 | 2.4 | |
GM-AEmA-GM-AEm (anhydro) |2 | 19.66±0.01 | 0.381±0.028 | 1773.738 | 1773.741 | 2.1 | |
Dimers | GM-AEmA-GM-AEmAG|2 | 15.33±0.02 | 0.179±0.005 | 1921.822 | 1921.826 | 2.2 |
29.54%±0.46% | GM-AEm-GM-AEmKR (anhydro) |2 | 18.07±0.01 | 0.170±0.024 | 1986.896 | 1986.900 | 2.1 |
GM-AEm-GM-AEm (anhydro) |2 | 18.77±0.01 | 0.141±0.015 | 1702.697 | 1702.704 | 4.5 | |
GM-AEmA-GM-AEmAA|2 | 16.54±0.01 | 0.075±0.002 | 1935.838 | 1935.842 | 2.1 | |
GM-AEm-GM-AEmG|2 | 13.91±0.01 | 0.054±0.003 | 1779.747 | 1779.752 | 2.7 | |
GM-GM-AEmA-GM-AEmA|2 | 17.51±0.01 | 0.046±0.028 | 2342.976 | 2342.985 | 3.6 | |
GM-AEmA-GM-AEmA (deacetyl) |2 | 15.17±0.01 | 0.029±0.022 | 1822.789 | 1822.794 | 3.0 | |
GM-AEmA-GM-AEmG (anhydro) |2 | 19.12±0.01 | 0.021±0.001 | 1830.761 | 1830.763 | 0.7 | |
GM-AEmA-GM-AEmAG (anhydro) |2 | 19.73±0.01 | 0.019±0.002 | 1901.796 | 1901.800 | 2.1 | |
GM-AEmA-GM-AEmAA (anhydro) |2 | 21.17±0.02 | 0.015±0.002 | 1915.812 | 1915.816 | 1.8 | |
GM-GM-AEmA-GM-AEm|2 | 16.85±0.00 | 0.003±0.004 | 2271.943 | 2271.947 | 2.1 | |
GM-AEmA-GM-AEmA-GM-AEmA|3 | 18.86±0.01 | 1.751±0.221 | 2788.192 | 2788.202 | 3.5 | |
GM-AEmA-GM-AEmA-GM-AEm|3 | 18.23±0.21 | 0.371±0.031 | 2717.158 | 2717.164 | 2.2 | |
GM-AEmA-GM-AEmA-GM-AEmA (anhydro) |3 | 22.39±0.02 | 0.222±0.027 | 2768.169 | 2768.175 | 2.3 | |
GM-AEmA-GM-AEmA-GM-AEmKR|3 | 17.54±0.01 | 0.207±0.028 | 3001.350 | 3001.360 | 3.4 | |
GM-AEmA-GM-AEmA-GM-AEm (anhydro) |3 | 21.60±0.02 | 0.117±0.003 | 2697.133 | 2697.138 | 1.8 | |
Trimers | GM-AEmA-GM-AEmA-GM-AEmKR (anhydro) |3 | 20.90±0.16 | 0.088±0.026 | 2981.328 | 2981.334 | 2.2 |
2.94%±0.36% | GM-AEmA-GM-AEmA-GM-AEmG|3 | 17.72±0.01 | 0.039±0.004 | 2774.182 | 2774.186 | 1.4 |
GM-AEmA-GM-AEm-GM-AEm|3 | 17.45±0.01 | 0.029±0.005 | 2646.123 | 2646.127 | 1.7 | |
GM-AEmA-GM-AEm-GM-AEm (anhydro) |3 | 21.16±0.01 | 0.025±0.001 | 2626.096 | 2626.101 | 1.9 | |
GM-AEmA-GM-AEm-GM-AEmKR|3 | 17.11±0.01 | 0.022±0.002 | 2930.316 | 2930.323 | 2.7 | |
GM-AEmA-GM-AEmA-GM-AEmAG|3 | 18.24±0.01 | 0.021±0.001 | 2845.217 | 2845.223 | 2.0 | |
GM-AEmA-GM-AEmA-GM-AEmAA|3 | 19.23±0.01 | 0.014±0.002* | 2859.235 | 2859.239 | 1.3 | |
GM-AEmA-GM-AEm-GM-AEmKR (anhydro) |3 | 20.31±0.02 | 0.014±0.005 | 2910.293 | 2910.297 | 1.5 | |
GM-AEm-GM-AEmG-GM-AEmAG|3 | 17.18±0.00 | 0.004±0.005 | 2703.143 | 2703.149 | 2.0 | |
GM-AEmA-GM-AEm-GM-AEmG (anhydro) |3 | 21.21±0.02 | 0.011±0.003* | 2754.157 | 2754.160 | 1.1 | |
GM-AEmA-GM-AEmA-GM-AEmAG (anhydro) |3 | 21.77±0.01 | 0.006±0.004 | 2825.189 | 2825.197 | 2.8 |
Inferrred dimers and trimers are based on the most abundant monomers and could correspond to alternative structures.
G: GlcNAc; M: MurNAc; m: meso-diaminopimelic acid; the number following the symbol ‘|’ refers to the oligomerisation state (1 for monomers, 2 for dimers, and 3 for trimers).
Calculated from two values.
E. coli simple mass database.
E. coli matching output and consolidated data.
MS/MS analysis of E. coli glycan chains and monomers.
E. coli complex mass database.
E. coli muropeptide complex table.
Inferred structure | Mass | ∆ppm | MaxQuant | ||
---|---|---|---|---|---|
Theoretical | Observed | This work | Anderson et al. | ||
GM (anhydro) | 478.1799 | 478.1780 | 4.0 | –2.7 | + |
GM | 498.2061 | 498.2042 | 3.9 | –4.2 | + |
GM (x2) (deacetyl) | 934.3755 | 934.3706 | 5.3 | –8.6 | + |
GM (x2) (anhydro) | 956.3598 | 956.3551 | 5.0 | 6.0 | + |
GM (x2) | 976.3860 | 976.3794 | 6.7 | –6.1 | + |
GM (x3) (deacetyl) | 1412.5554 | 1412.5490 | 4.5 | –6.2 | + |
GM (x3) (anhydro) | 1434.5397 | 1434.5348 | 3.4 | –7.5 | + |
GM (x3) | 1454.5659 | 1454.5592 | 4.6 | –5.3 | + |
GM (x4) | 1932.7458 | 1932.7352 | 5.5 | –5.1 | + |
GM-AE (anhydro) | 678.2596 | 678.2567 | 4.3 | –9.1 | + |
GM-AE | 698.2858 | 698.2830 | 3.9 | –12.9 | + |
GM-AEJ (anhydro) | 850.3444 | 850.3401 | 5.1 | –10.6 | + |
GM-AEJ | 870.3706 | 870.3676 | 3.5 | –5.9 | + |
GM-AEJA (anhydro) | 921.3815 | 921.3765 | 5.4 | –9.9 | + |
GM-AEJG | 927.3920 | 927.3868 | 5.6 | –8.9 | + |
GM-AEJA | 941.4077 | 941.4045 | 3.4 | –5.0 | + |
GM-AEJC | 973.3843 | 973.3763 | 8.2 | –2072.2 | + |
GM-AEJL | 983.4593 | 983.4498 | 9.6 | –15.5 | + |
GM-AEJK | 998.4703 | 998.4624 | 8.0 | –10.6 | + |
GM-AEJM | 1001.4153 | 1001.4060 | 9.2 | –13.5 | + |
GM-AEJAA | 1012.4448 | 1012.4413 | 3.4 | –7.8 | + |
GM-AEJY (anhydro) | 1013.4091 | 1013.4242 | –14.9 | 17.8 | + |
GM-AEJF | 1017.4433 | 1017.4347 | 8.4 | –15.0 | + |
GM-AEJY | 1033.4353 | 1033.4278 | 7.2 | –5.3 | + |
GM-AEJAV | 1040.4808 | 1040.4716 | 8.8 | –14.7 | + |
GM-AEJIA | 1054.4964 | 1054.4874 | 8.5 | –11.3 | + |
GM-AEJW | 1056.4394 | 1056.4455 | –5.8 | 4.0 | + |
GM-AEJAM | 1072.4524 | 1072.4460 | 5.9 | –4.3 | + |
GM-AEJKR | 1154.5667 | 1154.5631 | 3.1 | –8.1 | + |
GM-GM-AE | 1176.4836 | 1176.4590 | 20.9 | –24.7 | + |
GM-GM-AEJ | 1348.5684 | 1348.5457 | 16.9 | –24.9 | + |
GM-GM-AEJA | 1419.6055 | 1419.5824 | 16.2 | –23.5 | + |
GM-AEJA-GM-AEJ (amidase product) | 1313.5721 | 1313.5674 | 3.5 | –11.0 | + |
GM-AEJA-GM-AEJA (amidase product) | 1384.6092 | 1384.6037 | 4.0 | –7.4 | + |
GM-AEJ-GM-AEJ (anhydro) | 1702.7042 | 1702.6976 | 3.9 | 38.3 | + |
GM-AEJ-GM-AEJ | 1722.7304 | 1722.7234 | 4.1 | –8.6 | + |
GM-AEJA-GM-AEJ (double anhydro) | 1753.7151 | 1753.7043 | 6.2 | –7.2 | + |
GM-AEJA-GM-AEJ (anhydro) | 1773.7413 | 1773.7339 | 4.2 | –11.1 | + |
GM-AEJA-GM-AEJ | 1793.7675 | 1793.7596 | 4.4 | –8.8 | + |
GM-AEJA-GM-AEJA (dacetyl) | 1822.7941 | 1822.7808 | 7.3 | –7.4 | + |
GM-AEJA-GM-AEJA (double anhydro) | 1824.7601 | 1824.7447 | 8.4 | –15.6 | + |
GM-AEJA-GM-AEJA (anhydro) | 1844.7784 | 1844.7704 | 4.3 | –8.3 | + |
GM-AEJA-GM-AEJG | 1850.7889 | 1850.8158 | –14.6 | 9.7 | + |
GM-AEJA-GM-AEJA | 1864.8046 | 1864.7962 | 4.5 | –6.6 | + |
GM-AEJA-GM-AEJK (anhydro) | 1901.8410 | 1901.8297 | 5.9 | –14.5 | + |
GM-AEJA-GM-AEJL | 1906.8562 | 1906.8452 | 5.8 | –11.3 | + |
GM-AEJA-GM-AEJK | 1921.8672 | 1921.8586 | 4.5 | –12.0 | + |
GM-AEJA-GM-AEJF | 1940.8402 | 1940.8263 | 7.2 | –8.8 | + |
GM-AEJA-GM-AEJY | 1956.8322 | 1956.8210 | 5.7 | –7.6 | + |
GM-AEJA-GM-AEJAL | 1977.8933 | 1977.8813 | 6.0 | –10.7 | + |
GM-AEJA-GM-AEJKR | 2077.9636 | 2077.9589 | 2.2 | –13.0 | + |
GM-GM-AEJ-GM-AEJ | 2200.9282 | 2200.9000 | 12.8 | –17.7 | + |
GM-GM-AEJA-GM-AEJ | 2271.9653 | 2271.9368 | 12.6 | –18.4 | + |
GM-GM-AEJA-GM-AEJA | 2343.0024 | 2342.9734 | 12.4 | 411.4 | + |
GM-AEJA-GM-AEJA-GM-AEJ (double anhydro) | 2677.1120 | 2677.1000 | 4.5 | –10.7 | + |
GM-AEJA-GM-AEJA-GM-AEJ (anhydro) | 2697.1382 | 2697.1259 | 4.6 | –8.6 | + |
GM-AEJA-GM-AEJA-GM-AEJ | 2717.1644 | 2717.1532 | 4.1 | –10.7 | + |
GM-AEJA-GM-AEJA-GM-AEJA (double anhydro) | 2748.1491 | 2748.1363 | 4.7 | –11.0 | + |
GM-AEJA-GM-AEJA-GM-AEJA (anhydro) | 2768.1753 | 2768.1674 | 2.9 | –11.2 | + |
GM-AEJA-GM-AEJA-GM-AEJA | 2788.2015 | 2788.1919 | 3.4 | –9.7 | + |
GM-AEJA-GM-AEJA-GM-AEJK (anhydro) | 2825.2379 | 2825.2205 | 6.1 | –9.3 | + |
GM-GM-AEJA-GM-AEJA-GM-AEJ | 3195.3622 | 3195.3264 | 11.2 | –14.0 | + |
GM-GM-AEJA-GM-AEJA-GM-AEJA | 3266.3993 | 3266.3630 | 11.1 | –12.5 | + |
Alternative structures were matched:
GM-AEJ-GM-AEJK.
GM-AEJ-GM-AEJKA (anhydro).
GM-AEJ-GM-AEJKA.
GM-AEJ-GM-AEJA-GM-AEJKA (anhydro).
Pseudomonas aeruginosa matched muropeptides not reported previously.
Raw output of automated search using MaxQuant and PGFinder.
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Strain, strain background(Escherichia coli) | BW25113 | https://doi.org/10.1073/pnas.120163297 | RRID:Addgene_72340 | Model strain for PG analysis |
Strain, strain background(Clostridioides difficile) | R20291 | https://doi.org/10.1128/JB.0073107 | Model strain for PG analysis | |
Strain, strain background(Clostridioides difficile) | M7404 | https://doi.org/10.1371/journal.ppat.1002317 | Model strain for PG analysis | |
Software, algorithm | PGFinderv.0.02 | This work | Used for MS1 analysis of PG structure | |
Software, algorithm | Byosv.3.9–32 | Protein Metrics Inc | Used for MS data deconvolution and MS/MS analysis | |
Software, algorithm | MaxQuant v2.0.1.0 | Cox and Mann, 2008 | RRID:SCR_014485 | Used for MS data deconvolution |
Software, algorithm | Perseusv.1.6.10.53 | Tyanova et al., 2016 | RRID:SCR_015753 | Used statistical analysis of muropeptide abundance |
Step by step strategy for PG analysis.