Journal: Nature Communications

Article Title: Ion suppression correction and normalization for non-targeted metabolomics

doi: 10.1038/s41467-025-56646-8

Figure Lengend Snippet: a The IROA ion suppression correction workflow. b Number of MSTUS peaks detected across analytical conditions. c–k Raw MSTUS-12C (blue lines) and suppression-corrected MSTUS-12C (red lines) values are shown for: c HILIC positive mode, uncleaned source; d HILIC positive mode, clean source; e HILIC negative mode, uncleaned source; f HILIC negative mode, clean source; g RPLC positive mode, uncleaned source; h RPLC positive mode, clean source; ( i ) RPLC negative mode, uncleaned source; j RPLC negative mode, clean source; and k IC negative mode, cleaned source. l Ratio of raw MSTUS-12C to suppression-corrected MSTUS-12C peak intensity across chromatographic methods and experimental conditions. m Raw and suppression-corrected phenylalanine values in RPLC positive ionization mode with cleaned source. n Raw and suppression-corrected pyroglutamylglycine values in IC negative ionization mode. o Identified chemical composition in entire RPLC clean dataset, as an example. p Kohonen Self Organizing Maps (SOM) show suppression patterns in the RPLC Clean raw dataset for all 539 compounds. q Density map shows compounds associated with each of the patterns discovered in ( o ). r Raw MSTUS-12C (blue lines) and suppression-corrected MSTUS-12C (red lines) values are shown for RPLC positive mode and RPLC negative mode ( s ) for urine. t Ratio of raw MSTUS-12C to suppression-corrected 12 C peak intensity for urine matrix in positive and negative ion modes. u Plasma and urine MSTUS-12C signals for 4 common metabolites before and after suppression correction. 12C SC = 12C suppression corrected MSTUS; 13C raw = 13C raw MSTUS. Colors represent percent peak intensity as indicated by the color bar. Source data are provided as a Source Data file. Data are shown as mean ± s.d. ( c – n , r , s ).

Article Snippet: Using the IROA Workflow, analysts can err on the side of injecting larger sample volumes to ensure robust measurement of low-abundance analytes while simultaneously performing ion suppression correction to achieve more accurate results.

Techniques: Hydrophilic Interaction Liquid Chromatography

Journal: Nature Communications

Article Title: Ion suppression correction and normalization for non-targeted metabolomics

doi: 10.1038/s41467-025-56646-8

Figure Lengend Snippet: a Optimization of cancer cell count for the IROA-IS ion suppression correction workflow. Raw MSTUS-12C (blue lines), suppression-corrected MSTUS-12C (red lines), and DUAL-MSTUS normalized (green lines) values are shown for: b RPLC positive mode, cleaned source; and c RPLC negative mode, clean source. d Optimization of IROA-IS during extraction and during reconstitution for ion suppression correction workflow. e Identified chemical composition in OVCAR-8 cell using IROA-IS in extraction solvent for entire RPLC clean dataset by both positive and negative mode. f Identified chemical composition in OVCAR-8 cell using IROA-IS as reconstitute solvent for entire RPLC clean dataset by both positive and negative mode. g Identified chemical composition in OVCAR-4 cell using IROA-IS in extraction solvent for entire RPLC clean dataset by both positive and negative mode. h Identified chemical composition in OVCAR-4 cell using IROA-IS as reconstitute solvent for entire RPLC clean dataset by both positive and negative mode. i Percent coefficient of variation (%CV) for raw, suppression-corrected, and normalized data from OVCAR-8 cell using IROA-IS in extraction solvent for entire RPLC clean dataset by both positive and negative mode. j Percent coefficient of variation (%CV) for raw, suppression-corrected, and normalized data from OVCAR-8 cell using IROA-IS as reconstitute solvent for entire RPLC clean dataset by both positive and negative mode. k Percent coefficient of variation (%CV) for raw, suppression-corrected, and normalized data from OVCAR-4 cell using IROA-IS in extraction solvent for entire RPLC clean dataset by both positive and negative mode. l Percent coefficient of variation (%CV) for raw, suppression-corrected, and normalized data from OVCAR-4 cell using IROA-IS as reconstitute solvent for entire RPLC clean dataset by both positive and negative mode. Percent coefficient of variation (%CV) for non-IROA-driven raw, and IROA-driven raw, suppression-corrected, and normalized data from OVCAR-4 ( m ) and OVCAR-8 ( n ) cell lines, respectively, for entire RPLC clean dataset by both positive and negative mode. Colors represent percent peak intensity as indicated by the color bar. Source data are provided as a Source Data file. Data are shown as mean ± s.d. ( b , c ).

Article Snippet: Using the IROA Workflow, analysts can err on the side of injecting larger sample volumes to ensure robust measurement of low-abundance analytes while simultaneously performing ion suppression correction to achieve more accurate results.

Techniques: Cell Counting, Extraction, Solvent

Journal: bioRxiv

Article Title: Detection of genome-wide low-frequency mutations with Paired-End and Complementary Consensus Sequencing (PECC-Seq) revealed end-repair derived artifacts as residual errors

doi: 10.1101/2019.12.22.886440

Figure Lengend Snippet: Overview of PECC-Seq. ( A ) Library preparation. A PCR-free library construction workflow was applied with prolonged ultrasonic shearing process to construct libraries with shortened fragment sizes. ( B ) Paired-end Sequencing. In the shortened library fragments, overlaps between the paired-end reads were obtained. ( C ) Reads processing. Mapping coordinates and mapping orientations served as endogenous tags to extract the consensus read groups. As the two templates arising from the DNA duplex were reverse complementary, the two pairs of reads shared same mapping coordinates (dashed lines) while the mapping orientations were opposite (the directions of R1 and R2). By utilizing the information in the overlap (the red frame), total 4 reads with identical information could be obtained to form duplex consensus sequences. ( D ) Creating concensus sequences and removing sequencing errors. At the given position, any variant that only occurred in part of the 4 bases was considered as an error and removed. Only positions with 4 identical bases would be included to make consensus sequences for further mutation analysis.

Article Snippet: After treatment, genomic DNA of TK6 was extracted with the mtDNA extractor CT kit (WAKO, Osaka, Japan) and subjected to library preparation following the Illumina TruSeq DNA PCR-Free library preparation workflow with the prolonged ultrasonic shearing procedure to generate shorter double-stranded library fragments.

Techniques: Construct, Sequencing, Variant Assay, Mutagenesis