bims-mascan 2024-06-16 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2024–06–16
nine papers selected by
Giovanny Rodríguez Blanco, Uniklinikum Graz

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.
A workflow for targeted proteomics assay development using a versatile linear ion trap.
Quantifying acyl-chain diversity in isobaric compound lipids containing monomethyl branched-chain fatty acids.
Hybrid Quadrupole Mass Filter - Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.
Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics.
Exploiting ferroptosis vulnerabilities in cancer.
Advances in Chromatographic and Mass Spectrometric Techniques for Analyzing Reducing Monosaccharides and Their Phosphates in Biological Samples.
The Bioenergetic Landscape of Cancer.
Blood to Biomarker Quantitation in Under One Hour with Rapid Proteomics using a Hyperthermoacidic Protease.

bioRxiv. 2024 May 30. pii: 2024.05.25.595875. [Epub ahead of print]

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.

Kai Li, Guo Ci Teo, Kevin L Yang, Fengchao Yu, Alexey I Nesvizhskii.

Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (m/z, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved "pseudo-MS/MS" spectra, facilitating direct ("spectral-library free") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from cerebrospinal fluid (CSF) and plasma samples, data from phosphoproteomics and HLA immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass offset searches.

DOI: https://doi.org/10.1101/2024.05.25.595875
bioRxiv. 2024 Jun 01. pii: 2024.05.31.596891. [Epub ahead of print]

A workflow for targeted proteomics assay development using a versatile linear ion trap.

Ariana E Shannon, Rachael N Teodorescu, Nojoon Soon, Lilian R Heil, Cristina C Jacob, Philip M Remes, Mark P Rubinstein, Brian C Searle.

Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.

DOI: https://doi.org/10.1101/2024.05.31.596891
bioRxiv. 2024 May 28. pii: 2024.05.28.596332. [Epub ahead of print]

Quantifying acyl-chain diversity in isobaric compound lipids containing monomethyl branched-chain fatty acids.

C R Green, M J Kolar, G H McGregor, A T Nelson, M Wallace, C M Metallo.

Compound lipids comprise a diverse group of metabolites present in living systems, and metabolic- and environmentally-driven structural distinctions across this family is increasingly linked to biological function. However, methods for deconvoluting these often isobaric lipid species are lacking or require specialized instrumentation. Notably, acyl-chain diversity within cells may be influenced by nutritional states, metabolic dysregulation, or genetic alterations. Therefore, a reliable, validated method of quantifying structurally similar even-, odd-, and branched-chain acyl groups within intact compound lipids will be invaluable for gaining molecular insights into their biological functions. Here we demonstrate the chromatographic resolution of isobaric lipids containing distinct combinations of straight-chain and branched-chain acyl groups via ultra-high-pressure liquid chromatography (UHPLC)-mass spectrometry (MS) using a C30 liquid chromatography column. Using metabolically-engineered adipocytes lacking branched-keto acid dehydrogenase A (Bckdha), we validate this approach through a combination of fatty acid supplementation and metabolic tracing using monomethyl branched-chain fatty acids and valine. We observe resolution of numerous isobaric triacylglycerols and other compound lipids, demonstrating the resolving utility of this method. This approach strengthens our ability to quantify and characterize the inherent diversity of acyl chains across the lipidome.

DOI: https://doi.org/10.1101/2024.05.28.596332
bioRxiv. 2024 Jun 01. pii: 2024.05.31.596848. [Epub ahead of print]

Hybrid Quadrupole Mass Filter - Radial Ejection Linear Ion Trap and Intelligent Data Acquisition Enable Highly Multiplex Targeted Proteomics.

Philip M Remes, Cristina C Jacob, Lilian R Heil, Nicholas Shulman, Brendan X MacLean, Michael J MacCoss.

Targeted mass spectrometry (MS) methods are powerful tools for selective and sensitive analysis of peptides identified by global discovery experiments. Selected reaction monitoring (SRM) is currently the most widely accepted MS method in the clinic, due to its reliability and analytical performance. However, due to limited throughput and the difficulty in setting up and analyzing large scale assays, SRM and parallel reaction monitoring (PRM) are typically used only for very refined assays of on the order of 100 targets or less. Here we introduce a new MS platform with a quadrupole mass filter, collision cell, linear ion trap architecture that has increased acquisition rates compared to the analogous hardware found in the Orbitrap™ Tribrid™ series instruments. The platform can target more analytes than existing SRM and PRM instruments - in the range of 5000 to 8000 peptides per hour. This capability for high multiplexing is enabled by acquisition rates of 70-100 Hz for peptide applications, and the incorporation of real-time chromatogram alignment that adjusts for retention time drift and enables narrow time scheduled acquisition windows. Finally, we describe a Skyline external software tool that implements the building of targeted methods based on data independent acquisition chromatogram libraries or unscheduled analysis of heavy labeled standards. We show that the platform delivers ~10x lower LOQs than traditional SRM analysis for a highly multiplex assay and also demonstrate how analytical figures of merit change while varying method duration with a constant number of analytes, or by keeping a constant time duration while varying the number of analytes.

DOI: https://doi.org/10.1101/2024.05.31.596848
Anal Chem. 2024 Jun 12.

Wideband PRM: Highly Accurate and Sensitive Method for High-Throughput Targeted Proteomics.

Dowoon Nam, Minyoung Ji, Chaewon Kang, Hokeun Kim, Hyunju Yang, Kwon Hee Bok, Jingi Bae, Jiwon Hong, Sang-Won Lee.

Targeted mass spectrometry (MS) approaches, which are powerful methods for uniquely and confidently quantifying a specific panel of proteins in complex biological samples, play a crucial role in validating and clinically translating protein biomarkers discovered through global proteomic profiling. Common targeted MS methods, such as multiple reaction monitoring (MRM) and parallel-reaction monitoring (PRM), employ specific mass spectrometric technologies to quantify protein levels by comparing the transitions of surrogate endogenous (ENDO) peptides with those of stable isotope-labeled (SIL) peptide counterparts. These methods utilizing amino acid analyzed (AAA) SIL peptides warrant sensitive and precise measurements required for targeted MS assays. Compared with MRM, PRM provides higher experimental throughput by simultaneously acquiring all transitions of the target peptides and thereby compensates for different ion suppressions among transitions of a target peptide. However, PRM still suffers different ion suppressions between ENDO and SIL peptides due to spray instability, as the ENDO and SIL peptides were monitored at different liquid chromatography (LC) retention times. Here we introduce a new targeted MS method, termed wideband PRM (WBPRM), that is designed for high-throughput targeted MS analysis. WBPRM employs a wide isolation window for simultaneous fragmentation of both ENDO and SIL peptides along with multiplexed single ion monitoring (SIM) scans for enhanced MS sensitivity of the target peptides. Compared with PRM, WBPRM was demonstrated to provide increased sensitivity, precision, and reproducibility of quantitative measurements of target peptides with increased throughput, allowing more target peptide measurements in a shortened experiment time. WBPRM is a straightforward adaptation to a manufacturer-provided MS method, making it an easily implementable technique, particularly in complex biological samples where the demand for higher precision, sensitivity, and efficiency is paramount.

DOI: https://doi.org/10.1021/acs.analchem.4c00518
Nat Cell Biol. 2024 Jun 10.

Exploiting ferroptosis vulnerabilities in cancer.

Toshitaka Nakamura, Marcus Conrad.

Ferroptosis is a distinct lipid peroxidation-dependent form of necrotic cell death. This process has been increasingly contemplated as a new target for cancer therapy because of an intrinsic or acquired ferroptosis vulnerability in difficult-to-treat cancers and tumour microenvironments. Here we review recent advances in our understanding of the molecular mechanisms that underlie ferroptosis and highlight available tools for the modulation of ferroptosis sensitivity in cancer cells and communication with immune cells within the tumour microenvironment. We further discuss how these new insights into ferroptosis-activating pathways can become new armouries in the fight against cancer.

DOI: https://doi.org/10.1038/s41556-024-01425-8
Crit Rev Anal Chem. 2024 Jun 10. 1-23

Advances in Chromatographic and Mass Spectrometric Techniques for Analyzing Reducing Monosaccharides and Their Phosphates in Biological Samples.

Jiaqi Chen, Yifeng Lou, Yuwei Liu, Bowen Deng, Zheng Zhu, Sen Yang, Di Chen.

  Reducing monosaccharides and their phosphates are critical metabolites in the central carbon metabolism pathway of living organisms. Variations in their content can indicate abnormalities in metabolic pathways and the onset of certain diseases, necessitating their analysis and detection. Reducing monosaccharides and their phosphates exhibit significant variations in content within biological samples and are present in many isomers, which makes the accurate quantification of reducing monosaccharides and their phosphates in biological samples a challenging task. Various analytical methods such as spectroscopy, fluorescence detection, colorimetry, nuclear magnetic resonance spectroscopy, sensor-based techniques, chromatography, and mass spectrometry are employed to detect monosaccharides and phosphates. In comparison, chromatography and mass spectrometry are highly favored for their ability to simultaneously analyze multiple components and their high sensitivity and selectivity. This review thoroughly evaluates the current chromatographic and mass spectrometric methods used for detecting reducing monosaccharides and their phosphates from 2013 to 2023, highlighting their efficacy and the advancements in these analytical technologies.

Keywords:  Reducing monosaccharides; biological samples; chromatography; chromatography-mass spectrometry; detection techniques; mass spectrometry; sugar phosphates

DOI:  https://doi.org/10.1080/10408347.2024.2364232
Mol Metab. 2024 Jun 12. pii: S2212-8778(24)00097-8. [Epub ahead of print] 101966

The Bioenergetic Landscape of Cancer.

Elizabeth R M Zunica, Christopher L Axelrod, L Anne Gilmore, Erich Gnaiger, John P Kirwan.

  Bioenergetic remodeling of core energy metabolism is essential to the initiation, survival, and progression of cancer cells through exergonic supply of adenosine triphosphate (ATP) and metabolic intermediates, as well as control of redox homeostasis. Mitochondria are evolutionarily conserved organelles that mediate cell survival by conferring energetic plasticity and adaptive potential. Mitochondrial ATP synthesis is coupled to the oxidation of a variety of substrates generated through diverse metabolic pathways. As such, inhibition of the mitochondrial bioenergetic system by restricting metabolite availability, direct inhibition of the respiratory Complexes, altering organelle structure, or coupling efficiency may restrict carcinogenic potential and cancer progression. Here, we review the role of bioenergetics as the principal conductor of energetic functions and carcinogenesis while highlighting the therapeutic potential of targeting mitochondrial functions.

Keywords:  Bioenergetics; Cancer; Cell Survival; Energy Transformation; Mitochondria

DOI:  https://doi.org/10.1016/j.molmet.2024.101966
bioRxiv. 2024 Jun 02. pii: 2024.06.01.596979. [Epub ahead of print]

Blood to Biomarker Quantitation in Under One Hour with Rapid Proteomics using a Hyperthermoacidic Protease.

Steven M Yannone, Vikas Tuteja, Olena Goleva, Donald Y M Leung, Aleksandr Stotland, Angel J Keoseyan, Nathan G Hendricks, Jennifer E Van Eyk, Simion Kreimer.

Multi-step multi-hour tryptic proteolysis has limited the utility of bottom-up proteomics for cases that require immediate quantitative information. The recently available hyperthermoacidic (HTA) protease "Krakatoa" digests samples in a single 5 to 30-minute step at pH 3 and >80 °C; conditions that disrupt most cells and tissues, denature proteins, and block disulfide reformation. The combination of quick single-step sample preparation with high throughput dual trapping column single analytical column (DTSC) liquid chromatography-mass spectrometry (LC-MS) achieves "Rapid Proteomics" in which the time from sample collection to actionable data is less than 1 hour. The presented development and systematic evaluation of this methodology found reproducible quantitation of over 160 proteins from just 1 microliter of whole blood. Furthermore, the preference of the HTA-protease for intact proteins over peptides allows for sensitive targeted quantitation of the Angiotensin I and II bioactive peptides in under half an hour. With these methods we analyzed serum and plasma from 53 individuals and quantified Angiotensin and proteins that were not detected with trypsin. This assessment of Rapid Proteomics suggests that concentration of circulating protein and peptide biomarkers could be measured in almost real-time by LC-MS.
TOC Figure: Rapid proteomics enables near real-time monitoring of circulating blood biomarkers. One microliter of blood is collected every 8 minutes, digested for 20 minutes, and then analyzed by targeted mass spectrometry for 8 minutes. This results in a 30-minute delay with datapoints every 8 minutes.

DOI: https://doi.org/10.1101/2024.06.01.596979