About

Kristina Johnson is an Assistant Professor in the Electrical and Computer Engineering department at Northeastern University, with a joint appointment in Communication Sciences and Disorders. Her research focuses on the intersection of neuroscience, engineering, and autism, aiming to revolutionize understanding of neurodevelopmental differences such as autism, intellectual disabilities, and genetic neurodevelopmental disorders. She leads the Neurodevelopmental Dynamics (NDD) Lab, which conducts multidisciplinary research working closely with individuals and families affected by these conditions to generate real-world impact. Johnson received her PhD in Media Arts & Sciences with a specialization in Affective Computing from the Massachusetts Institute of Technology in 2021. Her work includes advancing neuroscience through wearable devices and developing quantitative metrics of vocal communication for minimally-speaking individuals using mobile technology. She has been recognized with the NIH Career Development Award in 2024 and has contributed to research on affective ratings of nonverbal vocalizations, modeling real-world vocalizations, and transfer learning in affective computing. Her efforts also extend to educational initiatives, such as teaching engineering classes that empower individuals with disabilities through innovative projects like adaptive keyboards and sensor systems.

Research topics

• Chemistry
• Biochemistry
• Chromatography

Selected publications

• Top-Down Proteomic Analysis of Limited Samples Using Porous Layer Open Tubular Columns and High-Field Asymmetric Ion Mobility Spectrometry Coupled to Mass Spectrometry

  Analytical Chemistry · 2025-06-30 · 4 citations

  articleOpen access

  Despite significant recent progress in the field of mass spectrometry (MS)-based top-down proteomics (TDP), the analysis of limited samples is still a major challenge. Here, we explored the potential of ultralow flow (ULF) liquid chromatography (LC) porous layer open tubular (PLOT) columns interfaced with MS via high-field asymmetric waveform ion mobility spectrometry (FAIMS) to enable high-sensitivity TDP analysis of small populations of mammalian cells. The developed robust and easy-to-use platform delivered high reproducibility of retention times (RSD < 0.4%) and high separation performance for intact proteins (∼14-s peak full width at half-maximum and peak capacity of >125 for a 60 min effective gradient). The FAIMS-based experiments resulted in a ∼2-fold increase in identifications compared to the control experiments for ∼200 HeLa cell aliquots, i.e., 819 vs 454 proteins and 2645 vs 1305 proteoforms, respectively. The pilot ULF LC-MS analysis of six HeLa cells yielded 29 ± 3 proteins and 38 ± 2 proteoforms, on average, and a total of 44 proteins and 68 proteoforms. Data revealed a high degree of acetylation, methylation, phosphorylation, glycosylation, lactylation, and other relevant post-translational modifications. Notably, the presented protein identification results for limited samples are comparable to those of recent large-scale TDP studies of bulk samples, demonstrating the potential to enable informative single-cell TDP profiling.

  PublisherDOI

• The Impact of Standardized Respiratory Care Practices on Delivery Room Intubation Frequency and NICU Ventilator Days in VLBW Infants: A Quality Improvement Initiative

  American Journal of Perinatology · 2025-10-27

  article

  Chronic lung disease (CLD) is a common morbidity affecting very low birth weight (VLBW) infants, and exposure to mechanical ventilation in this population is a well-known risk factor. Our 2018 Vermont Oxford Network outcome report demonstrated an increase in the incidence of CLD from 2017 (15%) to 2018 (30.9%).In response, we convened a multidisciplinary team to review our practices. Starting with baseline data on our delivery room (DR) and initial ventilation practices, we developed a key driver diagram to guide change ideas. We implemented sequential interventions using Plan-Do-Study-Act (PDSA) cycles.From January 2017 through January 2022, 390 infants with birthweights < 1,500 g were admitted to our level IV NICU. Special cause variation was observed in our two-outcome metrics: percent of inborn VLBW infants intubated in the DR, lowering the center line from 44 to 18% and lowering the center line from 19 to 12 total ventilation days per 100 patient days in this same population.Implementing standardized respiratory care practices resulted in significantly decreasing DR intubation rates and total ventilation days in this vulnerable population. · Employing protective lung strategies in VLBW infants is effective in limiting lung injury and preventing the development of chronic lung disease.. · Implementation of a resuscitation bundle can improve standard processes in the delivery room.. · Prophylactic surfactant replacement continues to be practiced in neonatal units..

  PublisherDOI

• Charge variant analysis of intact monoclonal antibody reference standards using microfluidic capillary zone electrophoresis

  Journal of Pharmaceutical and Biomedical Analysis · 2025-12-07 · 1 citations

  article
  PublisherDOI

• Native Capillary Electrophoresis–Mass Spectrometry of Near 1 MDa Non‐Covalent GroEL/GroES/Substrate Protein Complexes

  Advanced Science · 2024-01-08 · 14 citations

  articleOpen access

  Abstract Protein complexes are essential for proteins' folding and biological function. Currently, native analysis of large multimeric protein complexes remains challenging. Structural biology techniques are time‐consuming and often cannot monitor the proteins' dynamics in solution. Here, a capillary electrophoresis‐mass spectrometry (CE–MS) method is reported to characterize, under near‐physiological conditions, the conformational rearrangements of ∽1 MDa GroEL upon complexation with binding partners involved in a protein folding cycle. The developed CE–MS method is fast (30 min per run), highly sensitive (low‐amol level), and requires ∽10 000‐fold fewer samples compared to biochemical/biophysical techniques. The method successfully separates GroEL 14 (∽800 kDa), GroEL 7 (∽400 kDa), GroES 7 (∽73 kDa), and NanA 4 (∽130 kDa) oligomers. The non‐covalent binding of natural substrate proteins with GroEL 14 can be detected and quantified. The technique allows monitoring of GroEL 14 conformational changes upon complexation with (ATPγS) 4–14 and GroES 7 (∽876 kDa). Native CE‐pseudo‐MS 3 analyses of wild‐type (WT) GroEL and two GroEL mutants result in up to 60% sequence coverage and highlight subtle structural differences between WT and mutated GroEL. The presented results demonstrate the superior CE–MS performance for multimeric complexes' characterization versus direct infusion ESI–MS. This study shows the CE–MS potential to provide information on binding stoichiometry and kinetics for various protein complexes.

  PublisherOA PDFDOI

• Single-cell omic molecular profiling using capillary electrophoresis-mass spectrometry

  TrAC Trends in Analytical Chemistry · 2023-06-01 · 29 citations

  articleOpen access
  PublisherOA PDFDOI

• Development of high-sensitivity CE-ESI-MS-based methods for proteomic profiling of limited samples and single cells

  2022-01-01

  dissertationOpen access1st authorCorresponding

  The mass spectrometry (MS)-based 'omics' approach to protein analysis enables high-throughput profiling of the proteome, providing a rich data set of protein identifications and abundances to probe global protein expression levels from cells, tissue, or other biological samples. The depth of proteome coverage is generally correlated with the amount of sample that is analyzed, which in many cases comprises microgram (µg) to milligram (mg) levels of starting protein amount for most informative coverage. The downside to high sample requirements is that the resulting measurements reflect a weighted average of protein levels from the bulk sample and lose any assessment of heterogeneity within the sample. Single-cell proteomics (SCP) can provide more detailed information about individual cells and reveal subtleties in cellular heterogeneity that have previously been masked by bulk sampling approaches. Achieving sufficient proteome coverage at the single-cell level to perform impactful biological research is a challenge that has fueled significant advances in all aspects of single-cell proteomic analysis. Additionally, for some types of samples, such as microbiopsies and rare cells, it is not feasible to obtain the amounts required for bulk analysis, making profiling of these mass-limited samples largely inaccessible without high-sensitivity proteomic techniques. This dissertation aims to exploit the strengths of capillary electrophoresis coupled to MS (CE-MS)-based technologies to develop innovative methods with improved sensitivity that can expand the capabilities of limited sample and single-cell proteomic analyses. Current state-of-the-art methods and strategies for limited sample and SCP, including sample processing techniques and high-sensitivity separations, are reviewed in Chapter 1. Chapters 2 and 3 explore the benefits of ultrasensitive CE-MS applied to bottom-up proteomic (BUP) analysis of low nanogram and sub-nanogram samples. First, a novel CE-MS-based bottom-up proteomics approach optimized for high sensitivity was described and compared with alternative ultrasensitive methods to highlight specific advantages for profiling post-translational modifications (PTMs) in limited samples. We hypothesized that ion mobility separation coupled with CE-MS would enable higher sensitivity in proteomic profiling. In Chapter 3, coupling ultrasensitive CE-MS with high-field asymmetric waveform mobility spectrometry (FAIMS) was investigated to achieve greater levels of proteome coverage from a low nanogram sample. For the analysis of intact proteins using the top-down proteomic (TDP) approach, we hypothesized that CE-MS-based methods present an ideal opportunity to inject intact cells and lyse directly in the separation capillary to minimize sample losses. The fourth chapter tests two different modes of cell injection for analysis of &lt;10 mammalian cells and single cells with on-capillary lysis followed by CE-MS analysis exhibiting significantly higher numbers of protein and proteoform identifications from a single mammalian cell than have previously been reported. The results shown in this work denote a substantial step forward for the field of single-cell top-down proteomics. The final chapter summarizes the work detailed in this dissertation and discusses promising future directions for SCP technologies and prospective applications for CE-MS-based methods in other areas of high-sensitivity protein characterization. --Author's abstract

  PublisherOA PDFDOI

• Capillary Electrophoresis Coupled to Electrospray Ionization Tandem Mass Spectrometry for Ultra-Sensitive Proteomic Analysis of Limited Samples

  Analytical Chemistry · 2022 · 40 citations

  1st authorCorresponding
  • Chemistry
  • Chromatography
  • Biochemistry

  In this work, we developed an ultra-sensitive CE-MS/MS method for bottom-up proteomics analysis of limited samples, down to sub-nanogram levels of total protein. Analysis of 880 and 88 pg of the HeLa protein digest standard by CE-MS/MS yielded ∼1100 ± 46 and ∼160 ± 59 proteins, respectively, demonstrating higher protein and peptide identifications than the current state-of-the-art CE-MS/MS-based proteomic analyses with similar amounts of sample. To demonstrate potential applications of our ultra-sensitive CE-MS/MS method for the analysis of limited biological samples, we digested 500 and 1000 HeLa cells using a miniaturized in-solution digestion workflow. From 1-, 5-, and 10-cell equivalents injected from the resulted digests, we identified 744 ± 127, 1139 ± 24, and 1271 ± 6 proteins and 3353 ± 719, 5709 ± 513, and 8527 ± 114 peptide groups, respectively. Furthermore, we performed a comparative assessment of CE-MS/MS and two reversed-phased nano-liquid chromatography (RP-nLC-MS/MS) methods (monolithic and packed columns) for the analysis of a ∼10 ng HeLa protein digest standard. Our results demonstrate complementarity in the protein- and especially peptide-level identifications of the evaluated CE-MS- and RP-nLC-MS-based methods. The techniques were further assessed to detect post-translational modifications and highlight the strengths of the CE-MS/MS approach in identifying potentially important and biologically relevant modified peptides. With a migration window of ∼60 min, CE-MS/MS identified ∼2000 ± 53 proteins on average from a single injection of ∼8.8 ng of the HeLa protein digest standard. Additionally, an average of 232 ± 10 phosphopeptides and 377 ± 14 N-terminal acetylated peptides were identified in CE-MS/MS analyses at this sample amount, corresponding to 2- and 1.5-fold more identifications for each respective modification found by nLC-MS/MS methods.

  PublisherOA PDFDOI

• Coupling High-Field Asymmetric Ion Mobility Spectrometry with Capillary Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry Improves Protein Identifications in Bottom-Up Proteomic Analysis of Low Nanogram Samples

  Journal of Proteome Research · 2022 · 28 citations

  1st authorCorresponding
  • Chemistry
  • Chromatography
  • Biochemistry

  In this work, we pioneered the assessment of coupling high-field asymmetric waveform ion mobility spectrometry (FAIMS) with ultrasensitive capillary electrophoresis hyphenated with tandem mass spectrometry (CE-MS/MS) to achieve deeper proteome coverage of low nanogram amounts of digested cell lysates. An internal stepping strategy using three or four compensation voltages per analytical run with varied cycle times was tested to determine optimal FAIMS settings and MS parameters for the CE-FAIMS-MS/MS method. The optimized method applied to bottom-up proteomic analysis of 1 ng of HeLa protein digest standard identified 1314 ± 30 proteins, 4829 ± 200 peptide groups, and 7577 ± 163 peptide spectrum matches (PSMs) corresponding to a 16, 25, and 22% increase, respectively, over CE-MS/MS alone, without FAIMS. Furthermore, the percentage of acquired MS/MS spectra that resulted in PSMs increased nearly 2-fold with CE-FAIMS-MS/MS. Label-free quantitation of proteins and peptides was also assessed to determine the precision of replicate analyses from FAIMS methods with increased cycle times. Our results also identified from 1 ng of HeLa protein digest without any prior enrichment 76 ± 9 phosphopeptides, 18% of which were multiphosphorylated. These results represent a 46% increase in phosphopeptide identifications over the control experiments without FAIMS yielding 2.5-fold more multiphosphorylated peptides.

  PublisherOA PDFDOI

• Development of Highly Sensitive LC–MS and CE–MS Methods for In-Depth Proteomic and Glycomic Profiling of Limited Biological Samples

  LCGC North America · 2022-08-01

  article

  nformative and deep proteomic and glycomic characterization of limited availability biological and medical samples has been a significant challenge. Here, we describe our current and recent efforts in advancing sample preparation as well as miniaturized electric field- and pressure-driven separation approaches interfaced with high-end mass spectrometry (MS) to enhance the sensitivity and depth of proteomic and glycomic profiling of several types of limited biological and clinically relevant samples.

  PublisherDOI

• On-capillary Cell Lysis Enables Top-down Proteomic Analysis of Single Mammalian Cells by CE-MS/MS

  Analytical Chemistry · 2022 · 76 citations

  1st authorCorresponding
  • Chemistry
  • Chromatography
  • Biochemistry

  = 4) lysed on the capillary and analyzed by CE-MS/MS demonstrated a range of 17-40 proteins and 23-50 proteoforms identified. An additional cell line, THP-1, was analyzed at the single-cell level, and proteoform abundances were compared to show the capabilities of single-cell TDP (SC-TDP) for assessing cellular heterogeneity. This study demonstrates the initial application of TDP in single-cell proteome-level profiling. These results represent the highest reported identifications from TDP analysis of a single HeLa cell and prove the tremendous potential for CE-MS/MS on-capillary sample processing for high sensitivity analysis of single cells and limited samples.

  PublisherOA PDFDOI

Frequent coauthors

• James I. Hagadorn

  12 shared

• David W. Sink

  Hartford Financial Services (United States)

  12 shared

• Alexander R. Ivanov

  Massachusetts Eye and Ear Infirmary

  7 shared

• Michal Greguš

  4 shared

• Shabnam Lainwala

  University of Connecticut

  4 shared

• Jennifer Trzaski

  Connecticut Children's Medical Center

  4 shared

• James W. Hagadorn

  4 shared

• Elizabeth Brownell

  4 shared

Education

• Ph.D. Chemistry, Chemistry

  Northeastern University

  2022

• B.S. Biochemistry, Chemistry

  Villanova University

  2014

Awards & honors

• 2024 NIH Career Development Award