EMSL @ ASMS

June 4 - 8, 2023

10:30 a.m. to 2:30 p.m.

Presenter: Mary Lipton

5:45 to 7 p.m. CST

Presiding: Yuri van der Burgt, Mowei Zhou
 

Top-down mass spectrometry (TDMS) provides unique and complementary information at the intact protein level that is commonly
masked when using bottom-up proteomic methods. Nevertheless, the community has experienced various challenges in adopting TDMS
strategies due to a lack of a "one size fits all" solution. The difficulty is exacerbated by many options for sample preparation protocols,
instrument parameters, and data analysis software, especially when dealing with complex samples. After the feedback from the 2022
workshop, the Consortium for Top-down Proteomics (CTDP) has established an Early Career Researcher (ECR) committee to help
identify opportunities and plan activities to address many of these challenges as a community.

In this workshop, we will first have ECR representatives: 1) present planned near-term activities about more expertise sharing, including
experimental protocols; 2) discuss the vision for the newly opened CTDP LinkedIn group for barrier-free communication; 3) discuss an
initiative to create "golden datasets" for software development with inputs from the community; 4) solicit ideas for further improvements
and new activities. This will be followed by an update about the CTDP initiative on an interlab study of capillary electrophoresis from
Alexander Ivanov, Liangliang Sun, and Kevin Jooss. Last, we will host an open panel discussion for the audience to ask questions and
suggest ideas.

5:45 to 7 p.m.

Presiding: Yuri Corilo and Leonard Nyadong

This workshop will focus on the role of mass spectrometry on the development of alternative energy technologies.

5:45 to 7:00 p.m. CST

Presiding: Aivett Bilbao, Stacy Malaker, and Julie Courraud

This workshop will focus on the career paths of women in mass spectrometry.

10:30 a.m. CST

Presenter: Ljiljana Paša-Tolić will present this poster on behalf of James M. Fulcher. 

Single-cell multiomics (scMultiomics) provides a holistic view of gene regulatory networks, cellular diversity, and temporal dynamics. However, transcriptome-proteome scMultiomics is limited to a few hundred (and often significantly fewer) protein targets that require intermediate antibodies to measure. To overcome this bottleneck, we developed a scMultiomics platform which enables global profiling of the transcriptome and proteome from same single-cells using RNA sequencing and mass spectrometry-based proteomics, respectively. This platform was demonstrated to quantify over 5000 genes, 2500 proteins, and 100 phosphopeptides per single-cell on average. Through the integration of proteomic, phosphoproteomic, and transcriptomic data to study Cdk1-mediated cell cycle arrest, we identified covarying protein/gene clusters that could infer novel protein-protein interactions and find yet-to-be described Cdk1 phosphosites important for mitotic processes.

2:30 p.m. CST

Presenter: Sarah (Sarai) Williams

Proteomics using bulk-scale and whole tissue profiling can provide exceptional measurement depth, but  these approaches only capture averages that obscure single-cell or regional heterogeneity. Therefore, discovery of new tissue-regulatory mechanisms or cell types requires isolation of smaller functional units, and manipulation of them requires significant down-scaling of processing volumes and contact surface area to minimize sample loss. To address these challenges, we developed nanodroplet Processing in One-pot for Trace Samples (nanoPOTS), integrated it with Laser-Capture Microdissection (LCM) and fluorescent Assorted Cell Sorting (FACS), and applied it to spatial, low-cell, and single-cell plant proteomics. We demonstrate our approach in studying developmental and tissue-region changes in Sorghum bicolor,  rhizobial-legume symbiote processes, and drought-induced impacts on single-protoplasts from Arabidopsis.

5:45 to 7:30 p.m. CST 

Presiding: David Butcher and Yuri Corilo

This workshop will focus on open, reproducible workflows for analyzing Fourier-transform ion cyclotron resonance mass spectrometry data.

10:30 a.m. - 2:30 p.m. CST

Presenter: William Kew

Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the leading choice for analysis of complex mixtures, such as natural organic matter (NOM). However, robust high-throughput workflows, necessary for analysis at scales (temporal, spatial), are challenging due to instrumental and data processing complexities. The latest instruments, featuring lower-field (7T) magnets with frequency-multiple detection, present additional challenges for complex mixture analysis due to increased spectral artifacts, i.e., undertones. Here, we present several concurrent efforts to develop more objective and reproducible workflows for instrument tuning and data analysis. We propose to develop a deep reinforcement learning (DRL) based framework for instrument tuning. Further, we explore the utility of hardware-based absorption mode (aFT) signal processing to enhance mass resolution.

10:30 a.m. to 2:30 p.m. CST

Presenter: Yu Mi Kwon

Human pancreas is a highly heterogenous organ that plays key roles in digestion and metabolic homeostasis. Spatially-resolved proteomics technologies are emerging as a powerful tool for understanding tissue cellular organization in their native microenvironment and identifying signaling events associated with cellular communications. In our previous work, we developed a spatial proteomic platform by integrating laser capture microdissection (LCM) and Nanodroplet processing in one pot for trace samples (nanoPOTS) and enabled unbiased mapping with 50-µm resolution. In this work, we further improved our platform and applied it to map a single pancreatic islet microenvironment in a three-dimensional (3D) manner. Combining spatial proteomic results and morphological features enabled us to gain more molecular insights into human pancreatic islets and various cell types.

9:30 a.m. CST

Presenter: Arunima Bhattacharjee

10:30 a.m. to 2:30 p.m. CST

Presenter: Gregory Vandergrift

Obtaining broad molecular coverage and overcoming sample topography of biological samples are longstanding challenges in mass spectrometry imaging (MSI). Herein, we compare matrix-assisted laser desorption/ionization (MALDI) and nanospray desorption electrospray ionization (nano-DESI) MSI in the context of molecular coverage. For both approaches, we use 21T FTICR-MS and absorption mode FT processing (aFT), resulting in ultrahigh mass resolution datasets that are ideally suited to investigate high molecular complexity. Further, we explore sample imprinting strategies, specifically for nano-DESI, to overcome sample topography challenges. In nano-DESI-MS, maintaining a liquid junction with the sample throughout the entire experiment is essential. Therefore, imprinting allows for indirect MSI from a topographically simplified surface and may extend MSI to a greater diversity of samples.

3:10 to 3:30 p.m. CST

Presenter: Chris Anderton