From a molecular perspective, enactors of function in biology are intact proteins that can be variably modified at the genetic, transcriptional, or post-translational level. Over the past 30 years, mass spectrometry (MS) has become a powerful method for the analysis of proteomes. Prevailing bottom-up proteomics operates at the level of the peptide, leading to issues with protein inference, connectivity, and incomplete sequence/modification information. Top-down proteomics (TDP), alternatively, applies MS at the proteoform level to analyze intact proteins with diverse sources of intramolecular complexity preserved during analysis. Fortunately, advances in prefractionation workflows, MS instrumentation, and dissociation methods for whole-protein ions have helped TDP emerge as an accessible and potentially disruptive modality with increasingly translational value. In this review, we discuss technical and conceptual advances in TDP, along with the growing power of proteoform-resolved measurements in clinical and translational research.

/pdf/progress-in-top-down-proteomics-and-the-analysis-of-4mewutpdc1.pdf

Progress in Top-Down Proteomics and the Analysis of Proteoforms

The unique properties of gold nanoparticles, their rich surface chemistry, and low toxicity as well as easy methods of synthesis have promoted conjugation of the particles with numerous biomolecules for site-specific delivery. Gold nanoparticles have multiple applications including photoablation, diagnostic imaging, radiosensitization, vaccine development, antioxidant, and multifunctional drug-delivery vehicles. These applications require an increasingly complex level of surface decoration in order to achieve efficacy, and limit off-target toxicity. This review will discuss the chemical and physical approaches commonly utilized in relation to surface decoration and the powerful system used to indicate success of the conjugation. Finally, we review the range of recent studies about covalent and noncovalent modes for conjugation of antibodies to the particle surface that aim to advance gold nanoparticle treatments and diagnostics toward the clinic.

Various methods of gold nanoparticles (GNPs) conjugation to antibodies

G-quadruplex oligonucleotide AS1411 as a cancer-targeting agent: Uses and mechanisms.

G-quadruplex oligonucleotide AS1411 as a cancer-targeting agent: Uses and mechanisms General subjects

In the post-genomics era, the study of proteins is critical for understanding cellular functions at the molecular level.1-5 Beyond the genetic code, the human proteome is greatly diversified by various genetic variations, alternative splicing of RNA transcripts, and post-translational modifi-cations (PTMs).6,7 In 2013, the term “proteoform” was designated to describe “all of the different molecular forms in which the protein product of a single gene can be found”,6 clearing up the confusion in nomenclature and joining research efforts to develop methodologies for pro-teoform characterization. Top-down proteomics, which analyzes intact proteins without digestion, has proved to be a premier technology for global and comprehensive analy-sis of proteoforms.4,8,9 The top-down approach retains in-tact protein mass information, providing a “bird’s-eye” view of the proteome and allowing for identification of novel proteoforms, in-depth sequence characterization, and quantification of disease-associated PTMs.4,8,9

/pdf/top-down-proteomics-ready-for-prime-time-4x07jcufas.pdf

Top-Down Proteomics: Ready for Prime Time?

Disclosed herein is a system and method for analyzing a specimen containing the proteome by mass spectrometry. The system includes a protein separation module; a matrix processing module; and a mass spectrometer module. The protein separation module, the matrix processing module and the mass spectrometer are in fluid communication with one another.

High throughput mass spectrometric analysis of proteome samples

System and method for high throughput mass spectrometric analysis of proteome samples

A fractionation method called gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) has been used to dramatically increase the number of proteins identified in top-down proteomic workflows; however, the technique involves the use of sodium dodecyl sulfate (SDS), a surfactant that interferes with electrospray ionization. Therefore, an efficient removal of SDS is absolutely required prior to mass analysis. Traditionally, methanol/chloroform precipitation and spin columns have been used, but they lack reproducibility and are difficult to automate. Therefore, we developed an in-line matrix removal platform to enable the direct analysis of samples containing SDS and salts. Only small molecules like SDS permeate a porous membrane and are removed in a manner similar to cross-flow filtration. With this device, near-complete removal of SDS is accomplished within 5 min and proteins are subsequently mobilized into a mass spectrometer. The new platform was optimized for the analysis of GELFrEE fractions enr...

/pdf/online-matrix-removal-platform-for-coupling-gel-based-2nvx4e0xre.pdf

Online matrix removal platform for coupling gel-based separations to whole protein electrospray ionization mass spectrometry.

https://stacks.cdc.gov/view/cdc/30832/cdc_30832_DS1.pdf

Tunable loading of oligonucleotides with secondary structure on gold nanoparticles through a pH-driven method.

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High throughput mass spectrometric analysis of proteome samples

System and method for high throughput mass spectrometric analysis of proteome samples

Online matrix removal platform for coupling gel-based separations to whole protein electrospray ionization mass spectrometry.

Tunable loading of oligonucleotides with secondary structure on gold nanoparticles through a pH-driven method.