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At least 37 records · Page 2

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

47 OTHER INSTRUMENTATION↗

Publisher Correction: Strongly-coupled quantum critical point in an all-in-all-out antiferromagnet

The original PDF version of the Article contained an error in the last sentence of the author affiliation information, which incorrectly read ‘Correspondence and requests for materials should be addressed to T.$.R. (e-mail: tfr@caltech.edu) or to Y.F. (e-mail: yejun@oist.jp)’. The correct version states ‘T.F.R.’ in place of “T.$.R.’. This has been corrected in the PDF version of the Article. The HTML version was correct from the time of publication.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Publisher Correction: Engineering bacterial vortex lattice via direct laser lithography

The original version of this Article contained errors in Fig. 2. In Fig. 2d, the label below the blue circle incorrectly read “S i,a (t) < 0” and should have read “S i,a (t) > 0”. Furthermore, the sequence of labels on the side of the bottom three panel in Fig. 2 from top to bottom incorrectly read “S 9,70 > 0, S 9,70 > 0, S 9,70 < 0”, and should have read “S 9,70 < 0, S 9,70 > 0, S 9,70 < 0”. Finally, in the legend to Fig. 2, the scale bar size description “Scale bar: 100 μm” was incorrectly placed in the description of panel c, and should have been placed in the description of panel d. These errors have been corrected in both the PDF and HTML versions of the Article.

59 BASIC BIOLOGICAL SCIENCES↗

Publisher Correction: Scaling of domain cascades in stripe and skyrmion phases

The original version of this Article contained an error in Fig. 4d, in which the label of the region to the left of the white dashed lines incorrectly read 'Order stripes'. The correct version states 'Disorder stripes'. This has been corrected in both the PDF and HTML versions of the Article.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Author Correction: Building a global alliance of biofoundries

The original version of this Comment contained errors in the legend of Figure 2, in which the locations of the fifteenth and sixteenth GBA members were incorrectly given as '(15) Australian Genome Foundry, Macquarie University; (16) Australian Foundry for Advanced Biomanufacturing, University of Queensland'. The correct version replaces this with '(15) Australian Foundry for Advanced Biomanufacturing (AusFAB), University of Queensland and (16) Australian Genome Foundry, Macquarie University'. This has been corrected in both the PDF and HTML versions of the Comment.

59 BASIC BIOLOGICAL SCIENCES↗

Author Correction: Chemical trends of deep levels in van der Waals semiconductors

The original version of this Article omitted the following from the Acknowledgements: This research was partially conducted at the Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility. This has now been corrected in both the PDF and HTML versions of the Article.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Author Correction: High-fidelity qutrit entangling gates for superconducting circuits

The original version of this Article contained an error in the second sentence of the Acknowledgements, which incorrectly read: ‘This work was supported by the Quantum Testbed Program of the Advanced Scientific Computing Research for Basic Energy Sciences program, Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231’. The correct version states ‘the Quantum Testbed Program of the Advanced Scientific Computing Research Division’ in place of ‘the Quantum Testbed Program of the Advanced Scientific Computing Research for Basic Energy Sciences program’. This has been corrected in both the PDF and HTML versions of the Article.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Author Correction: Proton irradiation-decelerated intergranular corrosion of Ni-Cr alloys in molten salt

In the original version of this article, numbers for the beam current densities were incorrectly given as 1.5, 2.0, and 2.5 mA cm -2 in various locations, instead of the correct values 0.3, 0.4, and 0.5 mA cm -2 . This was owing to a measurement error coming from the indirect correspondence between the Faraday cup and the beam profile monitor (BPM) on the accelerator as the proton beam traveling along the beamline resulted in mismatching between calculated values and real beam currents, which were obtained by ex-situ calibration. The following changes have been made in the correct version. The eighth sentence of the Results, and the figure legend of Fig. 2j state '0.3, 0.4, 0.5 mA cm -2 ' in place of '1.5, 2.0, 2.5 mA cm -2 '. The figure legend of Fig. 1j–l states '0.5, 0.4, 0.3 mA cm -2 ' in place of '2.5, 2.0, 1.5 mA cm -2 '. Figure 1e states '0.5 mA cm -2 ' in place of '2.5 mA cm -2 ', Fig. 1h states '0.4 mA cm -2 ' in place of '2.0 mA cm -2 ', and Fig. 1k states ‘0.3 mA cm -2 ' in place of ‘1.5 mA cm -2 '. Figure 2c states '0.5 mA cm -2 ' in place of '2.5 mA cm -2 ', Fig. 2d states '0.4 mA cm -2 ' in place of '2.0 mA cm -2 ', and Fig. 2e states '0.3 mA cm -2 ' in place of '1.5 mA cm -2 '. Figure 2j and k states ‘0.3 mA cm -2 ', '0.4 mA cm -2 ', '0.5 mA cm -2 ' in place of '1.5 mA cm -2 ', '2.0 mA cm -2 ', and '2.5 mA cm -2 ', respectively. The figure legend of Fig. 3b states '0.4 mA cm -2 ' in place of '2.0 mA cm -2 '. The figure legend of Supplementary Fig. 1 states '0.5 mA cm -2 ' in place of '2.5 mA cm -2 '. This has been corrected in the PDF and HTML versions of the Article.

36 MATERIALS SCIENCE↗

Author Correction: The role of manganese in CoMnO x catalysts for selective long-chain hydrocarbon production via Fischer-Tropsch synthesis

Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-024-54578-3, published online 27 November 2024. The original version of this Article omitted a line in the Acknowledgements section: Work at the Molecular Foundry was supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This has been now added into the last line of the acknowledgements section in both the PDF and HTML versions of the Article.

99 GENERAL AND MISCELLANEOUS↗

Author Correction: Transcription Factor 4 loss-of-function is associated with deficits in progenitor proliferation and cortical neuron content

Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-022-29942-w, published online 02 May 2022 In the version of the article initially published, the text “UCSD has filed a patent application (WO2022072709A1), in which F.P. and A.R.M. are inventors, containing some results regarding the TCF4 correction overexpression strategy described in this paper. The patent was published on 04-07-2022” was missing from the Competing interests section and has now been added to the HTML and PDF versions of the article.

99 GENERAL AND MISCELLANEOUS↗

Author Correction: Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota

Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-024-53784-3, published online 4 November 2024 In the version of this article initially published, Table 1 did not include the properties of the taxa being proposed or refer directly to another location in the main manuscript describing the properties. As such, the original manuscript did not comply with Rule 27 (2)(c) of the ICNP. Also, Table 1 listed the order Fervidibacterales as the nomenclatural type for the class Fervidibacteria, which violates latest emended version of Rule 15 stating that the nomenclatural type for a class must be a genus. Below we provide a modification of Table 1 containing protologues with these errors corrected. We have also changed the order of the taxa in the table to meet the most common ordering. (Table presented.) Taxon names proposed under the ICNP Proposed taxon Etymology Description Genus Fervidibacter Fer.vi.di.bac’ter. L. masc. adj. fervidus, hot, steaming; N.L. masc. n. bacter, a rod; N.L. masc. n. Fervidibacter, a hot rod Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the genus. Gram-stain-negative and diderm cell envelope structure. Ovoid- to rod-shaped morphology. Spores are not formed. The genus is a distinct phylogenetic lineage in the family Fervidibacteraceae, the order Fervidibacterales, and the class Fervidibacteria in the phylum Armatimonadota. The type species is Fervidibacter sacchariT. Species Fervidibacter sacchari sac’cha.ri. N.L. gen. n. sacchari, of sugar Hyperthermophilic, microaerophilic, facultatively anaerobic, and grows chemoheterotrophically on monosaccharides and polysaccharides. Cells are ovoid- to rod-shaped, Gram-stain negative, and are 0.9–1.3 µm in width and 1.6–3.6 µm in length. Grows between 65 and 87.5 °C and an optimum temperature of 80 °C, and a pH range of 6.5–8.6 with an optimum pH of 7.5. Grows at an optimum O2 concentration of 5–10%. Grows on D-arabinose, D-galactose, D-glucose, D-rhamnose, D-ribose, D-xylose, chondroitin sulfate, colloidal chitin, galactan, gellan gum, guar gum, karaya gum, locust bean gum, xantham gum, xyloglucan, β-glucan, glycogen, starch, AFEX-pretreated corn stover, miscanthus, sugarcane bagasse, acetate and casamino acids. Grows weakly on xyloglucan under fermentation conditions. The major fatty acids (>10%) are C16:0, C18:0 and/or cyclo-C17:0, and iso-C16:0. The major respiratory quinones (>10%) are MK-8 and MK-9. The isolate and genomes of the species have been recovered from geothermal springs in the Great Basin, Nevada, USA. GC content of genomes range between 51–52%. Subunits for both the high-affinity and low-affinity terminal oxidases are encoded in the genomes. Genomes also encode a Group 3d [NiFe] hydrogenase, which produces hydrogen as an electron sink for NAD+ regeneration. The type strain PD1T (= JCM 39283T = DSM 113467T) was isolated from Great Boiling Spring in Nevada, USA. Family Fervidibacteraceae Fer.vi.di.bac.te.ra’ce.ae. N.L. masc. n. Fervidibacter type genus of the family; L. suff. -aceae ending to denote a family; N.L. fem. pl. n. Fervidibacteraceae the family of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic, with high-affinity and/or low-affinity terminal oxidases present in the genomes. The oxidative pentose phosphate pathway and the tricarboxylic acid cycle are complete in genomes belonging to the family. The family is a distinct phylogenetic lineage in the order Fervidibacterales and the class Fervidibacteria in the phylum Armatimonadota. The type genus is Fervidibacter. Order Fervidibacterales Fer.vi.di.bac.te.ra’les. N.L. masc. n. Fervidibacter type genus of the order; L. suff. -ales ending to denote an order; N.L. fem. pl. n. Fervidibacterales the order of the genus Fervidibacter Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Fervidibacteria and relative evolutionary divergence supports delineation of this lineage as an order within the class Fervidibacteria and phylum Armatimonadota. The type genus is Fervidibacter. Class Fervidibacteria Fer.vi.di.bac.te’ri.a. N.L. masc. n. Fervidibacter type genus of the type order of the class; L. suff. -ia ending to denote a class; N.L. neut. pl. n. Fervidibacteria the class of the order Fervidibacterales Thermophilic or hyperthermophilic inhabitants of freshwater thermal environments. All members are likely polysaccharide-degrading chemoheterotrophs with numerous carbohydrate-active enzymes encoded in their genomes. Aerobic or strictly anaerobic. Phylogenomic placement of this lineage within the Armatimonadota and relative evolutionary divergence supports delineation of this lineage as a class within the Armatimonadota. The type genus is Fervidibacter. The error has not been corrected in the PDF or HTML versions of the Article.

Nou, Nancy O↗