Removal of Interference MS/MS Spectra for Accurate Quantification in Isobaric Tag-Based Proteomics

Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm

Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.

A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics

Multiplex proteomics using isobaric labeling tags has emerged as a powerful tool for the simultaneous relative quantification of peptides and proteins across multiple experimental conditions. However, the quantitative accuracy of the approach is largely compromised by ion interference, a phenomenon that causes fold changes to appear compressed. The degree of compression is generally unknown, and the contributing factors are poorly understood. In this study, we thoroughly characterized ion interference at the MS2 level using a defined two-proteome experimental system with known ground-truth. We discovered remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2 scans-a discrepancy that we found resolved by considering cofragmentation of peptide ions hidden within the spectral "noise" of the MS1 isolation window. To address this issue, we developed a regression modeling strategy to accurately predict reporter ion interference in any dataset. Finally, we demonstrate the utility of our procedure for improved fold change estimation and unbiased PTM site-to-protein normalization. All computational tools and code required to apply this method to any MS2 TMT dataset are documented and freely available.

New Set of Isobaric Labeling Reagents for Quantitative 16Plex Proteomics

Peptide labeling by isobaric tags is a powerful approach for the relative quantitative analysis of proteomes in multiple groups. There has been a revolution in the innovation of new isobaric reagents; however, great effort is being made to expand simultaneous labeling groups to identify more labeled peptides and reduce reporter ion signal suppression. We redesigned the original chemical structure of the deuterium isobaric amine-reactive tag developed in our laboratory. We optimized the synthetic pathway to create a new set of 16-plex isobaric tags (IBT-16plex). The novel reagent enabled almost complete labeling of peptides within 90 min, with all labeling reporter ions exhibiting comparable MS/MS signals. Compared to a typical 16plex reagent, TMTpro-16plex, the peptides and proteins identified by IBT-16plex in trypsinized HeLa cells were significantly increased by 14.8 and 8.6%, respectively. Moreover, differences in peptide abundance within 10-fold among multiple groups were barely suppressed in IBT-16plex, whereas the dynamic range in TMTpro-16plex-labeled groups was smaller. After quantitative examination of MCF7 cell proteins, IBT-16plex was confirmed as feasible and useful for evaluating protein responses of glucose-starved MCF7 cells to a glucose-rich medium.

Chemical isotope labeling for quantitative proteomics

Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.

Recent advances in isobaric labeling and applications in quantitative proteomics

Mass spectrometry (MS) has emerged at the forefront of quantitative proteomic techniques. Liquid chromatography-mass spectrometry (LC-MS) can be used to determine abundances of proteins and peptides in complex biological samples. Several methods have been developed and adapted for accurate quantification based on chemical isotopic labeling. Among various chemical isotopic labeling techniques, isobaric tagging approaches rely on the analysis of peptides from MS2-based quantification rather than MS1-based quantification. In this review, we will provide an overview of several isobaric tags along with some recent developments including complementary ion tags, improvements in sensitive quantitation of analytes with lower abundance, strategies to increase multiplexing capabilities, and targeted analysis strategies. We will also discuss limitations of isobaric tags and approaches to alleviate these restrictions through bioinformatic tools and data acquisition methods. This review will highlight several applications of isobaric tags, including biomarker discovery and validation, thermal proteome profiling, cross-linking for structural investigations, single-cell analysis, top-down proteomics, along with applications to different molecules including neuropeptides, glycans, metabolites, and lipids, while providing considerations and evaluations to each application.

Multi-omics approach reveals posttranscriptionally regulated genes are essential for human pluripotent stem cells

The effects of transcription factors on the maintenance and differentiation of human-induced or embryonic pluripotent stem cells (iPSCs/ESCs) have been well studied. However, the importance of posttranscriptional regulatory mechanisms, which cause the quantitative dissociation of mRNA and protein expression, has not been explored in detail. Here, by combining transcriptome and proteome profiling, we identified 228 posttranscriptionally regulated genes with strict upregulation of the protein level in iPSCs/ESCs. Among them, we found 84 genes were vital for the survival of iPSCs and HDFs, including 20 genes that were specifically necessary for iPSC survival. These 20 proteins were upregulated only in iPSCs/ESCs and not in differentiated cells derived from the three germ layers. Although there are still unknown mechanisms that downregulate protein levels in HDFs, these results reveal that posttranscriptionally regulated genes have a crucial role in iPSC survival.

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The posttranscriptionally regulated 20 genes are necessary for iPSC survival

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The proteins of HSPA8, EIF3D, and NCBP2 are quickly degraded in HDFs

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mRNA localization affects the protein amounts in most of the 20 genes

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Translation is repressed in HDFs despite mRNA binding to ribosomes

A stress-reduced passaging technique improves the viability of human pluripotent cells

Xeno-free culture systems have expanded the clinical and industrial application of human pluripotent stem cells (PSCs). However, reproducibility issues, often arising from variability during passaging steps, remain. Here, we describe an improved method for the subculture of human PSCs. The revised method significantly enhances the viability of human PSCs by lowering DNA damage and apoptosis, resulting in more efficient and reproducible downstream applications such as gene editing and directed differentiation. Furthermore, the method does not alter PSC characteristics after long-term culture and attenuates the growth advantage of abnormal subpopulations. This robust passaging method minimizes experimental error and reduces the rate of PSCs failing quality control of human PSC research and application.

Post-Deconvolution MS/MS Spectra Extraction with Data-Independent Acquisition for Comprehensive Profiling of Urinary Glucuronide-Conjugated Metabolome

Conjugation reactions are of critical significance in human metabolism. Identification of these conjugated metabolites is still challenging. Here, we propose a strategy, post-deconvolution MS/MS spectra extraction with data-independent acquisition (PDMS2E-DIA), to comprehensively profile the glucuronide-conjugated metabolome. PDMS2E-DIA enables the identification of conjugated and unconjugated metabolite pairs through neutral loss filtering combined with a significant change in abundance after the deconjugation reaction. Purified DIA MS/MS spectra were constructed by extracting MS/MS fragments shared between spectra derived from conjugated and unconjugated metabolites. The feasibility of this approach was first demonstrated by the identification of two glucuronide-conjugated metabolite standards spiked in urine samples. For human urine samples, 479 features were structurally annotated as potential glucuronide-conjugated metabolites, resulting in the identification of 211 metabolites. Fragment peaks derived from interferents were found to be removed by PDMS2E-DIA, which increased about 6 times the number of identified urine metabolites compared with those calculated from raw DIA deconvoluted MS/MS spectra. This approach was found to have great potential for identifying glucuronide-conjugated metabolites, as well as other kinds of chemical conjugations.

Grafting of iPS cell-derived tenocytes promotes motor function recovery after Achilles tendon rupture

Tendon self-renewal is a rare occurrence because of the poor vascularization of this tissue; therefore, reconstructive surgery using autologous tendon is often performed in severe injury cases. However, the post-surgery re-injury rate is relatively high, and the collection of autologous tendons leads to muscle weakness, resulting in prolonged rehabilitation. Here, we introduce an induced pluripotent stem cell (iPSC)-based technology to develop a therapeutic option for tendon injury. First, we derived tenocytes from human iPSCs by recapitulating the normal progression of step-wise narrowing fate decisions in vertebrate embryos. We used single-cell RNA sequencing to analyze the developmental trajectory of iPSC-derived tenocytes. We demonstrated that iPSC-tenocyte grafting contributed to motor function recovery after Achilles tendon injury in rats via engraftment and paracrine effects. The biomechanical strength of regenerated tendons was comparable to that of healthy tendons. We suggest that iPSC-tenocytes will provide a therapeutic option for tendon injury.

Combined Omics Approaches Reveal the Roles of Non-canonical WNT7B Signaling and YY1 in the Proliferation of Human Pancreatic Progenitor Cells

The proliferation of human pancreatic progenitor cells (PPCs) is critical for developing cell therapies for diabetes. Here, using transcriptome analysis combined with small interfering RNA (siRNA) screening, we revealed that WNT7B is a downstream growth factor of AT7867, a compound known to promote the proliferation of PPCs generated from human pluripotent stem cells. Feeder cell lines stably expressing mouse Wnt7a or Wnt7b, but not other Wnts, enhanced PPC proliferation in the absence of AT7867. Importantly, Wnt7a/b ligands did not activate the canonical Wnt pathway, and PPC proliferation depended on the non-canonical Wnt/PKC pathway. A comparison of the phosphoproteome in response to AT7867 or a newly synthesized AT7867 derivative uncovered the function of YY1 as a transcriptional regulator of WNT7B. Overall, our data highlight unknown roles of non-canonical WNT7B/PKC signaling and YY1 in human PPC proliferation and will contribute to the stable supply of a cell source for pancreatic disease modeling and therapeutic applications.

Extracellular nanovesicles for packaging of CRISPR-Cas9 protein and sgRNA to induce therapeutic exon skipping

Prolonged expression of the CRISPR-Cas9 nuclease and gRNA from viral vectors may cause off-target mutagenesis and immunogenicity. Thus, a transient delivery system is needed for therapeutic genome editing applications. Here, we develop an extracellular nanovesicle-based ribonucleoprotein delivery system named NanoMEDIC by utilizing two distinct homing mechanisms. Chemical induced dimerization recruits Cas9 protein into extracellular nanovesicles, and then a viral RNA packaging signal and two self-cleaving riboswitches tether and release sgRNA into nanovesicles. We demonstrate efficient genome editing in various hard-to-transfect cell types, including human induced pluripotent stem (iPS) cells, neurons, and myoblasts. NanoMEDIC also achieves over 90% exon skipping efficiencies in skeletal muscle cells derived from Duchenne muscular dystrophy (DMD) patient iPS cells. Finally, single intramuscular injection of NanoMEDIC induces permanent genomic exon skipping in a luciferase reporter mouse and in mdx mice, indicating its utility for in vivo genome editing therapy of DMD and beyond.