Scientists from CEITEC Masaryk University, together with colleagues from the United States, have discovered a critical vulnerability in bacteria: without the protein RimM, they recover only very slowly under nutrient limitation or after stress. The proper assembly of ribosomes – the cell’s protein factories – plays a key role in their ability to resume multiplication. These findings open up a new way to disrupt bacteria’s capacity to restart proliferation, which could in the future help medicine better combat infections.Every bacterium has one essential ability – when exposed to unfavourable conditions, it can slow down and survive until conditions improve. Once they do, it quickly resumes its activity. It is precisely in this process that scientists from CEITEC at Masaryk University have identified bacteria’s Achilles’ heel.The research team focused on the bacterium Escherichia coli and found that without the protein RimM, its cells recover from stress much less efficiently. Their ability to resume cell division is slow in such cases, as RimM is involved in the assembly of ribosomes – structures essential for the production of proteins required for cell survival. Without it, bacteria multiply much more slowly following stress.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_199d25ed9b.jpg" alt="CEITEC/Demo Lab: Bacteria’s Achilles’ Heel – Without a Key Protein, They Multiply Slowly: Cryo-EM micrograph of ribosomal particles dispersed in a thin layer of amorphous ice." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_199d25ed9b.jpg 207w," sizes="100vw" width="1600" height="1205">Using cryo-electron microscopy, the scientists observed how ribosomes behave in the absence of RimM. They found that ribosomes assemble slowly and in a disordered manner – particularly in regions critical for accurate reading of genetic information – effectively placing the cell in a kind of “waiting mode.” “We found that the protein RimM is much more important for bacteria than previously thought,” says first author <a target="_blank" rel="noopener noreferrer" href="https://www.ceitec.eu/ahmed-adel-ibrahim-hassona-hassan/u94046?page=publication">Ahmed H. Hassan</a>. “Without it, the bacterial cell struggles to return to normal function, as ribosomes mature only slowly.”<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_3_1e27130702.jpeg" alt="CEITEC: Bacteria’s Achilles’ Heel – Without a Key Protein, They Multiply Slowly: Ahmed H. Hassan." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_3_1e27130702.jpeg 235w," sizes="100vw" width="1600" height="1067">The study also revealed that under these conditions, bacteria activate a protective mechanism that prevents premature joining of incomplete ribosomal parts. Additional proteins are engaged to deliberately slow the process, reducing the risk of forming defective ribosomes. As a result, the bacterium eventually recovers, but much later than usual. This vulnerability – where bacteria without RimM operate in a slowed-down mode – could in the future be exploited in new therapeutic strategies against bacterial infections.RimM is commonly found in bacteria but does not occur in humans, which is a major advantage for drug development, including antibiotics. If scientists develop a drug that blocks this protein, it would affect only bacteria and not human cells. “Such a treatment could significantly hinder bacterial recovery after stress caused, for example, by antibiotics, thereby limiting their further spread without causing side effects in patients,” explains lead researcher <a target="_blank" rel="noopener noreferrer" href="https://www.ceitec.eu/gabriel-demo-ph-d/u92825">Gabriel Demo</a>.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_4_474572c812.jpeg" alt="CEITEC/Martin Indruch: Bacteria’s Achilles’ Heel – Without a Key Protein, They Multiply Slowly: Gabriel Demo." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_4_474572c812.jpeg 235w," sizes="100vw" width="1600" height="1067">The study, conducted in collaboration with scientists from Thomas Jefferson University, Columbia University, and the University of California, Riverside, was published in the journal <a target="_blank" rel="noopener noreferrer" href="https://www.nature.com/articles/s41467-026-71781-6">Nature Communications</a>.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_2_d3266ee9ec.jpg" alt="CEITEC/Ahmed H. Hassan: Bacteria’s Achilles’ Heel – Without a Key Protein, They Multiply Slowly: Model of ribosome assembly with identified factors (red and blue) that promote assembly in the absence of RimM." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_CEITEC_Achillova_pata_bakterii_bez_klicoveho_proteinu_se_mnozi_pomalu_2_d3266ee9ec.jpg 103w," sizes="100vw" width="1600" height="2423">

Bacteria’s Achilles’ Heel – Without a Key Protein, They Multiply Slowly 

This study investigates the impact of emitter positioning on signal intensity in nanoflow electrospray ionization mass spectrometry. By systematically varying emitter position in three dimensions, the authors demonstrate that signal robustness improves at greater distances along the z-axis, with consistent performance maintained within 1–2 mm of the optimal position.Signal behavior was consistent across the m/z range, indicating that precise repositioning for different analytes is unnecessary. These findings provide practical guidance for improving robustness and reproducibility in nanoflow LC–MS/MS proteomics workflows.<blockquote><h4>The original article</h4><h4><a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/jasms.5c00441">Regarding Emitter Positioning for Nanoflow Electrospray Ionization with a High-Capacity Inlet Capillary</a></h4>Noah M. Lancaster, Scott T. Quarmby, Katherine A. Overmyer, and Joshua J. Coon*J. Am. Soc. Mass Spectrom. 2026, 37, 3, 754–759<a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1021/jasms.5c00441">https://doi.org/10.1021/jasms.5c00441</a><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a></h6></blockquote>Selected sections from the article follow. Formats and hyperlinks were adapted from the original.<div>Owing to its high sensitivity, nanoflow electrospray liquid chromatography coupled with tandem mass spectrometry (nESI-LC-MS/MS) is widely used for protein sequence analysis. <a href="javascript:void(0);">(1,2)</a> Whereas high-flow electrospray sources typically have relatively fixed emitter alignments and are more robust to changes in emitter positioning, nESI sources frequently require manual alignment in three dimensions. <a href="javascript:void(0);">(3,4)</a> Since the number of ions reaching the MS system can vary depending on the location of the nESI emitter, positioning is a critical aspect of achieving robust and reproducible results.Multiple reports illustrate the relationship between emitter positioning and electrospray signal intensity; <a href="javascript:void(0);">(2,4−10)</a> however, these studies typically examine a single dimension or evaluate emitters and flow regimes not typical of shotgun proteomic workflows. To understand these relationships, we investigate here the effect of emitter positioning on signal intensity when using fused-silica capillaries with integrated emitters at a flow rate of 300 nL/min, a common choice across the field. <a href="javascript:void(0);">(11−17)</a> Experiments were conducted using an Orbitrap Ascend mass spectrometer, a notable example of instruments commonly used in proteome analysis, <a href="javascript:void(0);">(18)</a> which features a nanoflow source and asymmetric inlet capillary (high-capacity transfer tube, HCTT). This work represents, to our knowledge, the first report in the literature characterizing how emitter positioning impacts signal intensity for nanoflow electrospray ionization into an inlet capillary without radial symmetry.Since most nESI emitters are manually positioned, understanding the precision in positioning that is required could assist in reducing batch-to-batch variation that is common in larger proteomic experiments. Further, recent efforts to improve the throughput of proteome analysis feature the use of multiple columns with multiple emitters aligned with the source at the same time. <a href="javascript:void(0);">(19−23)</a> By performing measurements in all three dimensions, this report provides insight for implementing such a multiemitter setup.<h4>Experimental Section</h4>Emitter positioning measurements were performed by infusing BSA peptides at 300 nL/min into an <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/748">Orbitrap Ascend mass spectrometer</a> (Thermo Scientific) using a fused silica capillary (360 μm O.D, 75 μm I.D.) with integrated emitter (∼10 μm opening). <a href="javascript:void(0);">(24)</a> The emitter was aligned to the inlet using the source camera and the x/y/z micrometer on a NanoSpray Flex source (Thermo Scientific). The origin of the coordinate system used here was defined as the center of the inlet capillary opening. In particular, the z = 0 plane is orthogonal to the opening of the inlet capillary, and the x = 0 and y = 0 planes are parallel to the inlet capillary axis. Top- and side-view images of the starting position are shown in <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Figure S2</a>. Code used for data analysis is available at <a target="_blank" rel="noopener noreferrer" href="https://github.com/coongroup/EmitterPositioning">https://github.com/coongroup/EmitterPositioning</a>. Raw data is available at MassIVE accession number MSV000100165. Additional experimental and data analysis details are described in the <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Supporting Information</a>.<h4>Results and Discussion</h4>We characterized signal intensity dependence on emitter position for nanoflow electrospray by infusing a mixture of peptides generated via trypsin digestion of purified BSA in an Orbitrap-quadrupole linear ion trap hybrid mass spectrometer (Orbitrap Ascend Tribrid). To ensure LC–MS applicability, we used an emitter size (∼10 μm orifice) and flow rate (300 nL/min) identical to those typical of capillary LC–MS. <a href="javascript:void(0);">(11−17)</a> The resulting MS1 analysis produced numerous ions across the m/z range (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Figure S3</a>). We selected two of these ions, a doubly protonated species (LGEYGFQNALIVR at m/z 740.4) and a triply protonated species (RHPEYAVSVLLR at m/z 480.6), for their strong signal intensity and stability over the time range of the experiments here (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Figures S4 and S5</a>). With the above setup, we tracked those m/z peaks as a function of emitter position in three dimensions and recorded intensity distributions (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/jasms.5c00441#fig1">Figure 1</a>). <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/jasms.5c00441#fig1">Figure 1</a>C presents the ion signal across x-positions, where the x = 0 plane is aligned to the central axis of the inlet capillary and the dashed lines depict the MS inlet opening width in this dimension (0.6 mm, <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Figure S6</a>). <a href="javascript:void(0);">(25,26)</a> Strikingly, we observe that the signal is relatively stable and high across two millimeters of the x-dimension. Further, greater than 50% of the ion signal is retained at distances up to ∼five times the width of the inlet (i.e., full width half max (fwhm)). <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/jasms.5c00441#fig1">Figure 1</a>D presents the same concept but in the y-dimension, where good signal stability is also observed across a similar length of two millimeters; however, the larger inlet opening in the y-dimension (1.6 mm) does not appear to proportionally impact the width of the intensity distribution. The ion plume is roughly symmetrical in both x- and y-dimensions; <a href="javascript:void(0);">(8)</a> therefore, it is expected that the smaller inlet width in the x-dimension would have a higher probability of being in the high density region of the plume than in the y-dimension. Proportional to inlet opening, the x position of the emitter would consequently have less of an effect on the intensity than the y position. We note the intensity distributions appear to be slightly off-center; however, we find the centroids of the distributions (−0.1 and 0.3 mm, x- and y-respectively, <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Figure S7</a>) were within the tolerance of the micrometer. <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/jasms.5c00441#fig1">Figure 1</a>E presents the ion intensities as a function of emitter position in the z-dimension. Impressively, signal continues to be observed up to ∼7 mm removed from the inlet at levels close to 50% of the highest. Not surprisingly, the highest signal is observed at the closest position, but, as noted above, that signal gradually declines with increasing distance. The relative intensities of these two peptide ions remain fairly constant at all observed z positions (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Figure S8</a>). Overall, identical trends were observed for both peptides over all dimensions. As these peptides are fairly high signal intensity, we wanted to confirm that the trends reported here were not biased by signal saturation, so we extracted signal intensities for low intensity features and compared the x, y, and z intensity distributions (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/jasms.5c00441/suppl_file/js5c00441_si_001.pdf">Figure S9</a>). This analysis confirms that these two peptides are representative of global trends for our tryptic peptide sample.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/J_Am_Soc_Mass_Spectrom_2026_37_3_754_759_Figure_1_1_D_Positioning_Experiments_A_The_xyz_coordinate_system_used_for_this_study_c971dc3d2f.jpg" alt="J. Am. Soc. Mass Spectrom. 2026, 37, 3, 754–759: Figure 1. 1D Positioning Experiments. (A) The x/y/z coordinate system used for this study. (B) An x/y perspective of the inlet with coordinate definitions. (C) Intensity dependence on x-position for two selected peptides (at y = 0 and z = −0.9). Dotted lines indicate the estimated position of the inlet capillary edges. (D) Intensity dependence on y-position for two selected peptides (at x = 0 and z = −0.9). Dotted lines indicate the estimated position of the inlet capillary edges. (E) Intensity dependence on z-position for two selected peptides (at x = 0 and y = 0)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_J_Am_Soc_Mass_Spectrom_2026_37_3_754_759_Figure_1_1_D_Positioning_Experiments_A_The_xyz_coordinate_system_used_for_this_study_c971dc3d2f.jpg 94w," sizes="100vw" width="996" height="1652"><h4>Conclusions</h4>We report the dependence of peptide signal intensity on emitter positioning for nanoflow electrospray. Specifically, within 1–2 mm in any dimension, one can achieve reasonably consistent and robust signal. Distinct intensity profiles we observed here for the x- and y-dimensions likely arise from the asymmetric shape of the ion capillary. We demonstrate improved robustness of signal intensity to x/y variation at increasing z distances, an observation that will be helpful for positioning multiple emitters, for example. <a href="javascript:void(0);">(19−23)</a>We provide evidence that the effect of the emitter position on signal intensity does not strongly depend on the analyte for bottom-up proteomics analysis. This report provides insight into the role of emitter positioning on signal intensity for bottom-up proteomics and represents the first characterization of the effect of emitter position on electrospray signal intensity on an instrument with an inlet capillary lacking radial symmetry. Future areas of interest would be an examination of how trends vary across different flow rates or emitter types, as well as assessing how the exact intensity profiles vary across instruments with differences in their atmospheric interface.</div>

Regarding Emitter Positioning for Nanoflow Electrospray Ionization with a High-Capacity Inlet Capillary

In the week of May 4, the following webinars await you in the field of liquid phase and especially HPLC and LC/MS.<blockquote><h4><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinars">👉 DETAILS AND REGISTRATION IN THE WEBINARS SECTION</a></h4>👉 Search and filter in the largest global database with over 5 500 GC, LC, MS and spectroscopy webinars.</blockquote><h5>1. Merck: Recent Advances in Chromatographic Approaches in Characterizing Antibody-Drug Conjugates</h5><ul><li>Tu, 5.5.2026 16:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6146">Registration</a></li></ul>Explore advanced LC-MS and HIC strategies for comprehensive ADC characterization, including impurity profiling, DAR analysis, and MS-compatible workflows.<h5>2. 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Webinars LabRulezLCMS Week 19/2026

Regarding Emitter Positioning for Nanoflow Electrospray Ionization with a High-Capacity Inlet Capillary

Bacteria’s Achilles’ Heel – Without a Key Protein, They Multiply Slowly