More Like this

1. Recent technical progress in sample preparation and liquid-phase separation-mass spectrometry for proteomic analysis of mass-limited samples

   https://doi.org/10.1039/d1ay00171j  

   Yang, Zhichang; Sun, Liangliang (March 2021, Analytical Methods)

   null (Ed.)

   Mass spectrometry (MS)-based proteomics has enabled the identification and quantification of thousands of proteins from complex proteomes in a single experiment. However, its performance for mass-limited proteome samples ( e.g. , single cells and tissue samples from laser capture microdissection) is still not satisfying. The development of novel proteomic methodologies with better overall sensitivity is vital. During the last several years, substantial technical progress has been achieved for the preparation and liquid-phase separation-MS characterization of mass-limited proteome samples. In this review, we summarize recent technological progress of sample preparation, liquid chromatography (LC)-MS, capillary zone electrophoresis (CZE)-MS and MS instrumentation for bottom-up proteomics of trace biological samples, highlight some exciting applications of the novel techniques for single-cell proteomics, and provide a very brief perspective about the field at the end. 

   more » « less
2. Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

   https://doi.org/10.3390/ijms21082873  

   Chen, Chen; Hou, Jie; Tanner, John J.; Cheng, Jianlin (April 2020, International Journal of Molecular Sciences)

   Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous progress in the understanding of cellular mechanisms, disease progression, and the relationship between genotype and phenotype. Though many popular bioinformatics methods in proteomics are derived from other omics studies, novel analysis strategies are required to deal with the unique characteristics of proteomics data. In this review, we discuss the current developments in the bioinformatics methods used in proteomics and how they facilitate the mechanistic understanding of biological processes. We first introduce bioinformatics software and tools designed for mass spectrometry-based protein identification and quantification, and then we review the different statistical and machine learning methods that have been developed to perform comprehensive analysis in proteomics studies. We conclude with a discussion of how quantitative protein data can be used to reconstruct protein interactions and signaling networks. 

   more » « less
3. A Mini Review on Capillary Isoelectric Focusing-Mass Spectrometry for Top-Down Proteomics

   https://doi.org/10.3389/fchem.2021.651757  

   Xu, Tian; Sun, Liangliang (April 2021, Frontiers in Chemistry)

   null (Ed.)

   Mass spectrometry (MS)-based top-down proteomics (TDP) requires high-resolution separation of proteoforms before electrospray ionization (ESI)-MS and tandem mass spectrometry (MS/MS). Capillary isoelectric focusing (cIEF)-ESI-MS and MS/MS could be an ideal method for TDP because cIEF can enable separation of proteoforms based on their isoelectric points (pIs) with ultra-high resolution. cIEF-ESI-MS has been well-recognized for protein characterization since 1990s. However, the widespread adoption of cIEF-MS for the characterization of proteoforms had been impeded by several technical challenges, including the lack of highly sensitive and robust ESI interface for coupling cIEF to MS, ESI suppression of analytes from ampholytes, and the requirement of manual operations. In this mini review, we summarize the technical improvements of cIEF-ESI-MS for characterizing proteoforms and highlight some recent applications to hydrophobic proteins, urinary albumin variants, charge variants of monoclonal antibodies, and large-scale TDP of complex proteomes. 

   more » « less
4. MS-based proteomics for comprehensive investigation of protein O -GlcNAcylation

   https://doi.org/10.1039/d1mo00025j  

   Xu, Senhan; Sun, Fangxu; Tong, Ming; Wu, Ronghu (April 2021, Molecular Omics)

   null (Ed.)

   Protein O -GlcNAcylation refers to the covalent binding of a single N -acetylglucosamine (GlcNAc) to the serine or threonine residue. This modification primarily occurs on proteins in the nucleus and the cytosol, and plays critical roles in many cellular events, including regulation of gene expression and signal transduction. Aberrant protein O -GlcNAcylation is directly related to human diseases such as cancers, diabetes and neurodegenerative diseases. In the past decades, considerable progress has been made for global and site-specific analysis of O -GlcNAcylation in complex biological samples using mass spectrometry (MS)-based proteomics. In this review, we summarized previous efforts on comprehensive investigation of protein O -GlcNAcylation by MS. Specifically, the review is focused on methods for enriching and site-specifically mapping O -GlcNAcylated peptides, and applications for quantifying protein O -GlcNAcylation in different biological systems. As O -GlcNAcylation is an important protein modification for cell survival, effective methods are essential for advancing our understanding of glycoprotein functions and cellular events. 

   more » « less
5. Tandem‐trapped ion mobility spectrometry/mass spectrometry coupled with ultraviolet photodissociation

   https://doi.org/10.1002/rcm.9192  

   Liu, Fanny C.; Ridgeway, Mark E.; Winfred, J. S. Raaj Vellore; Polfer, Nicolas C.; Lee, Jusung; Theisen, Alina; Wootton, Christopher A.; Park, Melvin A.; Bleiholder, Christian (September 2021, Rapid Communications in Mass Spectrometry)

   RationaleTandem‐ion mobility spectrometry/mass spectrometry methods have recently gained traction for the structural characterization of proteins and protein complexes. However, ion activation techniques currently coupled with tandem‐ion mobility spectrometry/mass spectrometry methods are limited in their ability to characterize structures of proteins and protein complexes. MethodsHere, we describe the coupling of the separation capabilities of tandem‐trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS) with the dissociation capabilities of ultraviolet photodissociation (UVPD) for protein structure analysis. ResultsWe establish the feasibility of dissociating intact proteins by UV irradiation at 213 nm between the two TIMS devices in tTIMS/MS and at pressure conditions compatible with ion mobility spectrometry (2–3 mbar). We validate that the fragments produced by UVPD under these conditions result from a radical‐based mechanism in accordance with prior literature on UVPD. The data suggest stabilization of fragment ions produced from UVPD by collisional cooling due to the elevated pressures used here (“UVnoD2”), which otherwise do not survive to detection. The data account for a sequence coverage for the protein ubiquitin comparable to recent reports, demonstrating the analytical utility of our instrument in mobility‐separating fragment ions produced from UVPD. ConclusionsThe data demonstrate that UVPD carried out at elevated pressures of 2–3 mbar yields extensive fragment ions rich in information about the protein and that their exhaustive analysis requires IMS separation post‐UVPD. Therefore, because UVPD and tTIMS/MS each have been shown to be valuable techniques on their own merit in proteomics, our contribution here underscores the potential of combining tTIMS/MS with UVPD for structural proteomics. 

   more » « less