NewS

What is your current position and affiliation?
I am a project group leader (a position somewhat between postdoc and group leader) at the Max Planck Institute of Biochemistry within the group of Matthias Mann.

How would you like your work to contribute to the field of proteomics?
I currently focus on clinical mass spectrometry-based proteomics and nearly any project I am working on involves patient samples or is a direct collaboration with clinicians. I would like to continue employing this powerful method to uncover biological mechanisms and better understand diseases, which ultimately will benefit patients with better treatments. In the best case scenario, this leads for example to the discovery of novel biomarkers or therapeutic targets, but also a better functional understanding without the identification of distinct single biomarkers is a step in the right direction. Biomarker discovery is often done with large patient cohorts and I hope to contribute to the field by enabling such studies from a technical perspective and providing the community with unique datasets. In parallel to this work, I would like to transform proteomics from a method for biomarker discovery by retrospective analysis to a tool for pro- and diagnostics in the future.

What have you found in the HUPO community/congress?
I had the chance to attend the HUPO world congresses two times so far. I found it to be a perfect intersection of different interest groups forming a thriving community between biological expertise and technical solutions.

How was your experience/what did it mean to present your work at HUPO?
Having been invited to the ECR manuscript competition to HUPO in Busan to present my work meant a lot to me. Sharing the excitement about new findings is definitely a driver of motivation for me to work as a scientist and being given the opportunity to do so in such a venue has been a major pleasure. I received a plethora of positive feedback from this wonderful community, which is truly motivating.

REGISTER HERE

WEBINAR DESCRIPTION:

RPPA is a high-throughput protein array technology that simultaneously measures hundreds or thousands of samples on glass slides with high precision and reliability, using specific antibodies. RPPA and mass spectrometry-based protein profiling are complementary technologies for protein profiling. In attending this webinar, attendees will learn about RPPA's high-throughput capabilities and laser-captured microdissection technology. They will understand how these technologies precisely measure protein expression, modifications, and phosphorylation in tumor cells.

SPEAKER BIO:

Dr. Rosa Isela Gallagher obtained her Ph.D. in Cell and Molecular Biology from GMU in 2019. She has accumulated more than 15 years of expertise in Reverse Phase Protein Array (RPPA) and Laser Capture Microdissection (LCM) technologies and is currently a Senior Research Scientist in the Center for Applied Proteomics and Molecular Medicine, led by Drs. Lance Liotta and Emanuel Petricoin III, the inventors of both technologies. RPPA is a high-throughput, antibody-based protein array technology capable of conducting assays on small amount of materials on thousands of samples simultaneously. This platform measures protein expression levels and modifications, including phosphorylation. Dr. Gallagher’s current research focuses on the molecular profiling of tumor cells utilizing LCM and RPPA to investigate unique signaling pathway profiles and new disease mechanisms to guide diagnosis, prognosis, and targeted therapeutics.

REGISTER HERE

The December HUPOST is now available.....check out the ETC webinars, HPP Chair & Co-chair nominations, C-HPP updates, upcoming events & a farewell message from HUPOST editor Ben Garcia...

DATE: Wednesday, February 21, 2024
TIME: 7am PST / 10am EST / 4pm CET
LOCATION:  Zoom (link to follow upon registration)
SPEAKER:  Oliver Raether

SPEAKER BIO:

Oliver Raether is Research and Development Manager at Bruker Daltonics in Bremen. He received his M.Sc. in engineering from the Hamburg University of Technology (1995). Over the past nearly three decades he and his colleagues have developed orthogonal time of flight mass spectrometers including since 2010 the timsTOF product line. He has produced 14 peer reviewed journal articles and is inventor/co-inventor of 71 patents in the field of mass spectrometry and, more recently, ion mobility spectrometry (h-index 13). His awards include the HUPO Science and Technology Award for contributions on Trapped Ion Mobility Mass Spectrometry Instrumentation (2020).

REGISTER HERE

DATE: Wednesday, January 24, 2024
TIME: 6am PST / 9am EST / 3pm CET
LOCATION:  Zoom (link to follow upon registration)
SPEAKER: Daniel DeBord, PhD

WEBINAR DESCRIPTION:

Protein identification is of fundamental importance in many areas of proteomics. Its applications include determining the presence or absence of an expected protein in a sample of interest, identifying an unknown protein present in a biological sample, and identifying a protein responsible for biochemical activity in an isolated protein fraction. In some cases, mass spectrometry or affinity-based methods may be suitable options, but these methods can face substantial challenges. Scientists need the ability to identify and measure peptide modifications, structures, and impurities more definitively and faster. Driven by structures for lossless ion manipulation (SLIM) technology, the MOBIE® instrument’s high-resolution ion mobility mass spectrometry platform separates and identifies the most challenging molecules with unprecedented resolution without compromising speed. By combining the MOBIE® platform’s high-resolution ion mobility mass spectrometry (HRIM-MS) data with liquid chromatography, more accurate separation and identification of impurities and posttranslational modifications (PTMs) can be achieved, reducing run times and costs.

LEARNING OBJECTIVES:

1. Attendees will learn Attendees will learn about (1) separation science, including SLIM (structures for lossless ion manipulation) and high-resolution ion mobility (HRIM); (2) the trade-off between speed, resolution, and reproducibility; and (3) accuracy for targeted lipidomics, peptide characterization, glycan analysis, PFAS, and many other workflows.
2. Why Attend?  AAttendees will uncover insights into how to incorporate HRIM into traditional analytical workflows and where the technology is used to answer clinical questions.

SPEAKER BIO: 

REGISTER HERE

The Human Proteome Project (HPP) was launched in 2010 under the aegis of HUPO. The vision of HUPO is that HPP activities will collectively and ultimately lead to breakthroughs enabled by proteomics, in medicine, biotechnology and the life sciences, thereby leaving a legacy of human proteome research. 

The HPP continues to make progress, addressing three major components, Chromosome-HPP (C-HPP), Biology and Disease-HPP (BD-HPP) and the HPP-Grand Challenge. It is focused on:

1. Cataloguing the human protein ‘parts’ list with high accuracy.
2. Understanding the complexity and function of the human proteome (including post-translational modifications, splice variants, proteoforms, small proteins/peptides, etc.).
3. Document and provide data deposition and analysis globally through portals (e.g., ProteomeXchange) and via major specific efforts (e.g., Human Protein Atlas, PeptideAtlas, neXtProt) with communal guidelines/metrics published with an annual communal reanalysis of whole human proteome’s protein existence (PE) status and making proteomics an integrated complement across the clinical, biomedical and life sciences research space.
4. In 2021, the HPP inaugurated the establishment of the HPP Grand Challenge project “A function for every protein”. 

ROLES / RESPONSIBILITIES:

Chair

The HPP Chair leads the development and implementation of the Human Proteome activities of the C-HPP, the B/D-HPP and the HPP Grand Challenge. The term of the HPP Chair is two years and so the position becomes vacant on December 31, 2024. To ensure a smooth and consistent transition, the incoming Chair will sit on the HPP EC for one year (2024) prior to their 2-year term (2025-2026) and also be present as past Chair in 2027.

Co-chair

The HPP Co-Chair helps lead the development and implementation of the Human Proteome activities of the C-HPP, the B/D-HPP and the HPP Grand Challenge with the HPP Chair. The term of the HPP Co-Chair is two years and is staggered with appointment of the HPP Chair. The HPP Co-Chair position becomes vacant on December 31, 2023, for a 2-year term (2024-2025).

Responsibilities:

• Chair the HPP Executive Committee and work with the HPP strategic advisory group to maximize the impact of HPP
• Evolve and implement the strategic goals of the HPP by working with the HPP Executive Council and its membership to accelerate progress, assess the goals and performance of each component, and connect the components of the HPP
• Supporting all HPP initiatives (C-HPP, B/D-HPP) and the HPP Grand Challenge
• Represent the HPP on the HUPO Executive Committee monthly calls
• Represent the HPP at national/international/strategic meetings, as needed
• Liaison with other HUPO Committees (e.g., HUPO Marketing and HUPO Early Career Committee) and initiatives (e.g., Antibody and Single Cell) to support the development of science and education
• Work with HUPO External Development Committee (HEDI) and the HUPO EC to work on strategic projects and funding with other resources for the scientific community

QUALIFICATIONS

HUPO is currently seeking scientifically strong, strategic, vibrant, enthusiastic and collegial leaders who will be suitable candidates to lead, build, advance, and represent the HPP. HUPO is keen to ensure regional and gender equity across its management structures. This position is honorary and in line with the many organizational positions within the HUPO Executive Committee.

APPLICATIONS

All candidates must be active HUPO members and scientists from the public or private sector with professional experience in the educational, research, or commercial activities related to the HPP. Applications will be accepted and a vote conducted. The successful candidate will be reviewed and approved by the HUPO Executive Committee.

To apply, please submit:

1. Your CV
2. A recent photo (in JPEG high-resolution format)
3. A statement of the position in which you are applying
4. A one-page vision statement outlining why you are a suitable candidate for the position.

SUBMISSIONS

To: office@hupo.org

Deadline: December 15, 2023

QUESTIONS

Email Charles Pineau (current HPP Chair) charles.pineau@inserm.fr

AI Tools in Grant Writing Applications, Research Articles, CVs, etc.

Chairs: Emily Hashimoto-Roth (University of Toronto, Canada) and Ruth Huttenhain (Stanford University, USA)

Speakers:

• Dr. Laura Elo (University of Turku, Finland)
• Dr. Min-Sik Kim (Daegu Gyeongbuk Institute of Science & Technology, South Korea)
• Dr. Jack Washington (Molecular Omics, United Kingdom)

The session "AI tools in grant writing applications, research articles, CVs, etc." focused on the integration of new artificial intelligence (AI) technologies into various aspects of scientific document production and publication.

Attendees shared the utility of AI tools such as ChatGPT to enhance their daily work efficiency, mentioning that these tools are quite useful for brainstorming and idea generation. In particular, using ChatGPT as a writing aid was recognized as a valuable tool to overcome writer's block or "blank-page-o-phobia”. It was also discussed how AI tools can also be very useful for editing and proofreading, especially when English is not the writer’s first language. The potential use of AI by journals for proofreading to identify formatting and writing errors was also discussed, indicating the evolving role of AI in scientific publishing.

Participants also questioned mentors regarding best practices for AI tools in research. IN short it was mentioned that AI can be leveraged to polish visualization, troubleshoot software code, and even interpret results, but such tools should be used with caution. Despite the benefits of using ChatGPT prompts for writing, the need for critical review and manual editing to ensure the final written output meets scientific standards was emphasized. Ethical concerns, including the risk of data leaks when using AI tools for proofreading and the need for transparency of AI contributions was mentioned. Overall, the session shed light on the growing role of AI in proteomics research and the broader scientific publishing landscape. It offered an exploration on AI’s potential to enhance efficiency, address ethical concerns, and possibly reshape the way scientific research is published and shared in the future.

Promoting Your Science

Chairs: Daniel Garama (Hudson Institute of Medical Research, Australia) and Mathieu Lavallée-Adam (University of Ottawa, Canada)

Speakers:

• Dr. Alexey Nesvizhskii (University of Michigan, USA)
• Dr. Hyun Woo Park (Yonsei University, South Korea)
• Dr. Stephen Pennington (University College Dublin, Ireland)
• Paula Burton (Mass Dynamics, Australia)

This session explored the many aspects of promoting your science as well as how scientific outreach can help in advancing one’s career.

It was clearly highlighted during the session that one key aspect of promoting your science involves, identifying target audiences. In addition to attending specialized conferences, participants discussed alternative methods for identifying the right audience for their research. Strategies included utilizing social media, publishing in widely read journals, and engaging with interdisciplinary communities. The session touched on the topic of maintaining a professional online presence. While recognizing the value sharing elements of one’s personal life, participants advised caution about posting some personal photos online, emphasizing the usefulness of a separate professional profile to maintain a credible image.

Attendees also discussed the role of institutional support in self-promotion. Many shared how universities, institutes, and companies can provide resources, such as funding, mentorship, and networking opportunities, to aid in career advancement and science promotion. Interestingly, participants considered some of the challenges related with dealing with opposition. Speakers shared their experiences on how they find the courage and confidence to address opposition to their ideas and results. The importance of constructive feedback, resilience, and persistence was highlighted. Finally, the panelists emphasized the importance of diversity and inclusion efforts in academia and research.

Geographical Differences for Academic Job Applications

Chairs: Andreas Hober (AstraZeneca, Sweden) and Lívia Rosa-Fernandes (Macquarie University Centre for Motor Neuron Disease Research, Australia)

Speakers:

• Dr. Nicki Packer (Macquarie University, Australia)
• Dr. Uwe Völker (University Greifswald, Germany)
• Dr. Yu-Ju Chen (Academia Sinica, Taiwan)
• Dr. Birgit Schilling (Buck Institute, USA)

During this session, attendees learned about the added value of conducting research abroad. In particular the benefits of exposure to different scientific cultures and networking opportunities were highlighted. Still, it was acknowledged that working abroad is not a universal requirement for a successful career. International relocation can have profound effects on personal aspects, such as partnerships and family. For example, some participants were curious regarding the challenges faced by expecting or new parents in finding jobs. The conversation emphasized the importance of supportive and flexible work environments to accommodate family responsibilities.

Attendees discussed the current job demand in the proteomics field, recognizing its rapid growth with increasing opportunities in academia, industry, and healthcare. Tips were shared for students aspiring to secure positions, including reaching out to potential mentors and the importance of making a good impression during a job interview by attaining  to a professional etiquette. For graduate students interested in finding postdoctoral positions, panelists shared how most postdocs typically find their positions, highlighting networking, collaborations, and mentor recommendations as effective strategies. The timing of grant applications for postdoctoral researchers and beyond was a significant topic. Advice emphasized starting early, cultivating strong grant-writing skills, and being strategic.

In addition, participants acknowledged diverse career paths within proteomics research outside of the traditional academic route. These paths encompassed roles in scientific communication, project management, bioinformatics, and more. Some attendees expressed their interest in transitioning to industry and panelists debated the optimal timing for transitioning from academia to industry. It was agreed that this decision should be based on individual career goals and the alignment of research interests with industry demands.

The main goal of the new HUPO single-cell proteomics (SCP) initiative is to provide guidance and create a comparative overview of novel mass spectrometry (MS)-based low-input and single-cell technologies. After the first reports of SCP with large cells (i.e., oocytes) the field has quickly moved to ever more comprehensive analysis of single mammalian cells or even subcellular components.^1–3 A variety of workflows have since demonstrated valuable insights into cellular identities and their function, driven entirely by the proteome and their post-translational modifications.^4–6 However, deep proteome profiling of single mammalian cells or small subpopulations remains an analytical challenge for most non-specialized laboratories.

The growing interest in the SCP workflows and its application to biological questions has driven the initiation of this international SCP initiative. Our team is comprised of a diverse group of early, middle and advanced level scientists with growing expertise in diverse workflows and instrumentation. We aim to provide a comparative overview of current SCP approaches for the community to ease the implementation in more laboratories and integration to novel biological projects. Considering the ongoing trend away from bulk analysis towards resolving cellular heterogeneity, we believe that such unifying efforts will drive the understanding of complex tissue hierarchies and orchestrated spatiotemporal interactions.

To this end, our first goal is to perform a multi-laboratory study, processing the same batch of cells across different platforms and establish the first of such direct comparisons. We will leverage the knowledge of our SCP initiative members, who have pioneered various parts of the SCP workflows, including sample collection and preparation, chromatographic separation, acquisition strategies and analysis approaches.^2,3,7–9 We consider utilization of one cell batch especially important for these comparisons, as cell handling and the cell cycle heavily influence cell size and proteome composition.^5,10 Our portfolio of SCP workflows will include isobaric multiplexing (i.e. TMT) with one chemical label for multiple cells (i.e. carrier - SCoPE) to facilitate sufficient peptide signal even with less sensitive MS instrumentation.² Following tremendous improvements in instrument sensitivity and implementation of ion-mobility separation also label-free SCP workflows have been successfully demonstrated.^5,11 Those are typically paired with data independent acquisition (DIA), which massively reduces precursor stochasticity in comparison to data dependent acquisition.¹² Most standard TMT-based workflows rely on small isolation windows to reduce precursor co-isolation to relatively quantify a single precursor through their reporter ions.¹³ Scanning speeds of current instrumentation therefore restrict isobaric labeling workflows to DDA, which suffer from detrimental amounts of missing data across large sample cohorts.¹² The alternative label-free SCP approaches, however, are notoriously low in throughput as only once cell at a time is being analyzed in comparison to the isobaric labelling strategies (i.e. TMTpro = 18 samples or HyperSCP = 28).^14,15 As most applications for SCP require the analysis of hundreds or even thousands of cells, most recently a combination of non-isobaric chemical labeling with DIA allowing for relative quantification between up to three samples at the MS1 level was introduced.^16,17 This reduces missingness across a large number of samples while still increasing throughput through multiplexing.

As an alternative to chemical multiplexing, many groups aim to increase measurement throughput by optimizing chromatographic separation. Due to their low input, SCP samples do not require such extensive separation, allowing for the effective gradient length to be reduced in comparison to bulk.^5,18–22 Short gradients and most efficient inject-to-inject times has been implemented with the disposable trap columns of the Evosep One. Those are regularly used for SCP workflows, due to the combination of in-line clean up the sample and simultaneous separation of peptides, while the previous sample is still acquired on the MS.^5,23,24 SCP initiative team members also most recently demonstrated significantly reduced separation times employing non-commercial alternatives to increase chromatographic throughput.^18,21,22 Additionally, to the various acquisition and peptide separation efforts, the SCP community has proposed smart strategy to streamline sample preparation for reduced peptide losses and improved reproducibility.^{2,7,8,11,20,25–27} Our comparative analysis will therefore include both plate-based sample preparation at higher volumes (i.e. 1-3uL) and dedicated chip or slide based approaches with low nanoliter volumes within dedicated instruments such as the cellenONE and Tecan Uno.^{3,7,20,27–29}

The entire proteomics community, but especially researchers focusing on improvements in SCP, are heavily dependent on instrumentation sensitivity and throughput advances. The introduction of the Thermo Fisher Scientific Astral combining the Orbitrap and a novel asymmetric track lossless analyzer with optimized ion transfer and flight track design was readily awaited.^30–32 The combination of 200 Hz scanning speed in the Astral analyzer with the unprecedented resolution of the Orbitrap demonstrates great potential for profiling single cells.³² This now complements SCP studies regularly performed on earlier generation Orbitrap instruments, most recently linear ion trap analyzers and the highly sensitive time-of-flight instruments with trapped ion-mobility separation for operation at 100% duty cycle.^3,5,33,34 The latter has been updated this year to the Bruker Daltonics timsTOF Ultra with a more efficient ion source, allowing more ions to enter the instrument and thereby again boosting sensitivity, as well as improving dynamic range.^10,35 The combination of instrument vendors striving to improve sensitivity and throughput paired with the introduction of alternative acquisition strategies and outside the box thinking is pushing the field forward every day. Our SCP initiative therefore aims to support further development, provide a comparative overview of many techniques for multidisciplinary scientists and guide study design to make SCP more readily available for the scientific community.

Contributed by Dr. Budnik Bogdan, chair of the B/D-HPP single-cell initiative

References:

1.         Lombard‐Banek, C., Moody, S.A., and Nemes, P. (2016). Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus) Embryo. Angewandte Chemie International Edition 55, 2454–2458. 10.1002/anie.201510411.

2.         Budnik, B., Levy, E., Harmange, G., and Slavov, N. (2018). SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. Genome Biology 19. 10.1186/s13059-018-1547-5.

3.         Zhu, Y., Clair, G., Chrisler, W.B., Shen, Y., Zhao, R., Shukla, A.K., Moore, R.J., Misra, R.S., Pryhuber, G.S., Smith, R.D., et al. (2018). Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS. Angewandte Chemie International Edition 57, 12370–12374. 10.1002/anie.201802843.

4.         Specht, H., Emmott, E., Petelski, A.A., Huffman, R.G., Perlman, D.H., Serra, M., Kharchenko, P., Koller, A., and Slavov, N. (2021). Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biology 22, 50. 10.1186/s13059-021-02267-5.

5.         Brunner, A.-D., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., Hoerning, O.B., Bache, N., Apalategui, A., Lubeck, M., et al. (2022). Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation. Molecular Systems Biology 18, e10798. 10.15252/msb.202110798.

6.         Zhu, Y., Scheibinger, M., Ellwanger, D.C., Krey, J.F., Choi, D., Kelly, R.T., Heller, S., and Barr-Gillespie, P.G. (2019). Single-cell proteomics reveals changes in expression during hair-cell development. eLife 8, e50777. 10.7554/eLife.50777.

7.         Ctortecka, C., Hartlmayr, D., Seth, A., Mendjan, S., Tourniaire, G., and Mechtler, K. (2022). An automated workflow for multiplexed single-cell proteomics sample preparation at unprecedented sensitivity. 2021.04.14.439828. 10.1101/2021.04.14.439828.

8.         Schoof, E.M., Furtwängler, B., Üresin, N., Rapin, N., Savickas, S., Gentil, C., Lechman, E., Keller, U. auf dem, Dick, J.E., and Porse, B.T. (2021). Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nat Commun 12, 3341. 10.1038/s41467-021-23667-y.

9.         Végvári, Á., Rodriguez, J.E., and Zubarev, R.A. (2022). Single-Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death. Anal. Chem. 94, 9261–9269. 10.1021/acs.analchem.2c00413.

10.       Evosep (2023). AN-021A - Pushing-the-boundaries-for-robust-and-high-throughput-single-cell-proteomics.pdf. https://www.evosep.com/wp-content/uploads/2022/12/AN-021A-Pushing-the-boundaries-for-robust-and-high-throughput-single-cell-proteomics.pdf.

11.       Zhu, Y., Piehowski, P.D., Zhao, R., Chen, J., Shen, Y., Moore, R.J., Shukla, A.K., Petyuk, V.A., Campbell-Thompson, M., Mathews, C.E., et al. (2018). Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells. Nature Communications 9, 882. 10.1038/s41467-018-03367-w.

12.       Muntel, J., Kirkpatrick, J., Bruderer, R., Huang, T., Vitek, O., Ori, A., and Reiter, L. (2019). Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows with Fixed Instrument Time. J. Proteome Res. 18, 1340–1351. 10.1021/acs.jproteome.8b00898.

13.       Savitski, M.M., Mathieson, T., Zinn, N., Sweetman, G., Doce, C., Becher, I., Pachl, F., Kuster, B., and Bantscheff, M. (2013). Measuring and Managing Ratio Compression for Accurate iTRAQ/TMT Quantification. Journal of Proteome Research 12, 3586–3598. 10.1021/pr400098r.

14.       Liang, Y., Truong, T., Saxton, A.J., Boekweg, H., Payne, S.H., Van Ry, P.M., and Kelly, R.T. (2023). HyperSCP: Combining Isotopic and Isobaric Labeling for Higher Throughput Single-Cell Proteomics. Anal. Chem. 95, 8020–8027. 10.1021/acs.analchem.3c00906.

15.       Li, J., Cai, Z., Bomgarden, R.D., Pike, I., Kuhn, K., Rogers, J.C., Roberts, T.M., Gygi, S.P., and Paulo, J.A. (2021). TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing. J Proteome Res 20, 2964–2972. 10.1021/acs.jproteome.1c00168.

16.       Derks, J., Leduc, A., Wallmann, G., Huffman, R.G., Willetts, M., Khan, S., Specht, H., Ralser, M., Demichev, V., and Slavov, N. (2022). Increasing the throughput of sensitive proteomics by plexDIA. Nat Biotechnol, 1–10. 10.1038/s41587-022-01389-w.

17.       Thielert, M., Itang, E.C., Ammar, C., Rosenberger, F.A., Bludau, I., Schweizer, L., Nordmann, T.M., Skowronek, P., Wahle, M., Zeng, W.-F., et al. (2023). Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Molecular Systems Biology n/a, e11503. 10.15252/msb.202211503.

18.       Zheng, R., Matzinger, M., Mayer, R., Valenta, A., Sun, X., and Mechtler, K. (2023). A high-sensitivity low-nanoflow LC-MS configuration for high-throughput sample-limited proteomics. 2023.04.27.538542. 10.1101/2023.04.27.538542.

19.       Xiang, P., Zhu, Y., Yang, Y., Zhao, Z., Williams, S.M., Moore, R.J., Kelly, R.T., Smith, R.D., and Liu, S. (2020). Picoflow Liquid Chromatography–Mass Spectrometry for Ultrasensitive Bottom-Up Proteomics Using 2-μm-i.d. Open Tubular Columns. Anal. Chem. 92, 4711–4715. 10.1021/acs.analchem.9b05639.

20.       Matzinger, M., Müller, E., Dürnberger, G., Pichler, P., and Mechtler, K. (2022). Robust and easy-to-use one pot workflow for label free single cell proteomics. 2022.10.03.510693. 10.1101/2022.10.03.510693.

21.       Kreimer, S., Binek, A., Chazarin, B., Cho, J.H., Haghani, A., Hutton, A., Marbán, E., Mastali, M., Meyer, J.G., Mesquita, T., et al. (2023). High-Throughput Single-Cell Proteomic Analysis of Organ-Derived Heterogeneous Cell Populations by Nanoflow Dual-Trap Single-Column Liquid Chromatography. Anal. Chem. 95, 9145–9150. 10.1021/acs.analchem.3c00213.

22.       Webber, K.G.I., Truong, T., Johnston, S.M., Zapata, S.E., Liang, Y., Davis, J.M., Buttars, A.D., Smith, F.B., Jones, H.E., Mahoney, A.C., et al. (2022). Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform. Anal. Chem. 10.1021/acs.analchem.2c00646.

23.       Bache, N., Geyer, P.E., Bekker-Jensen, D.B., Hoerning, O., Falkenby, L., Treit, P.V., Doll, S., Paron, I., Müller, J.B., Meier, F., et al. (2018). A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics. Molecular & Cellular Proteomics 17, 2284–2296. 10.1074/mcp.TIR118.000853.

24.       Ye, Z., Sabatier, P., Martin-Gonzalez, J., Eguchi, A., Bekker-Jensen, D.B., Bache, N., and Olsen, J.V. (2023). One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes. 2023.08.10.552756. 10.1101/2023.08.10.552756.

25.       Johnson, K.R., Gao, Y., Greguš, M., and Ivanov, A.R. (2022). On-capillary Cell Lysis Enables Top-down Proteomic Analysis of Single Mammalian Cells by CE-MS/MS. Anal. Chem. 10.1021/acs.analchem.2c03045.

26.       Johnston, S.M., Webber, K.G.I., Xie, X., Truong, T., Nydegger, A., Lin, H.-J.L., Nwosu, A., Zhu, Y., and Kelly, R.T. (2023). Rapid, One-Step Sample Processing for Label-Free Single-Cell Proteomics. J. Am. Soc. Mass Spectrom. 34, 1701–1707. 10.1021/jasms.3c00159.

27.       Sanchez-Avila, X., Truong, T., Xie, X., Webber, K.G.I., Johnston, S.M., Lin, H.-J.L., Axtell, N.B., Puig-Sanvicens, V., and Kelly, R.T. (2023). Easy and Accessible Workflow for Label-Free Single-Cell Proteomics. J. Am. Soc. Mass Spectrom. 10.1021/jasms.3c00240.

28.       Leduc, A., Huffman, R.G., Cantlon, J., Khan, S., and Slavov, N. (2022). Exploring functional protein covariation across single cells using nPOP. Genome Biology 23, 261. 10.1186/s13059-022-02817-5.

29.       Dou, M., Clair, G., Tsai, C.-F., Xu, K., Chrisler, W.B., Sontag, R.L., Zhao, R., Moore, R.J., Liu, T., Pasa-Tolic, L., et al. (2019). High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform. Anal. Chem. 91, 13119–13127. 10.1021/acs.analchem.9b03349.

30.       Stewart, H., Grinfeld, D., Giannakopulos, A., Petzoldt, J., Shanley, T., Garland, M., Denisov, E., Peterson, A., Damoc, E., Zeller, M., et al. (2023). Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis. 2023.06.02.543408. 10.1101/2023.06.02.543408.

31.       Heil, L.R., Damoc, E., Arrey, T.N., Pashkova, A., Denisov, E., Petzoldt, J., Peterson, A., Hsu, C., Searle, B.C., Shulman, N., et al. (2023). Evaluating the performance of the Astral mass analyzer for quantitative proteomics using data independent acquisition. 2023.06.03.543570. 10.1101/2023.06.03.543570.

32.       Petrosius, V., Aragon-Fernandez, P., Arrey, T.N., Üresin, N., Furtwängler, B., Stewart, H., Denisov, E., Petzoldt, J., Peterson, A.C., Hock, C., et al. (2023). Evaluating the capabilities of the Astral mass analyzer for single-cell proteomics. 2023.06.06.543943. 10.1101/2023.06.06.543943.

33.       Phlairaharn, T., Ye, Z., Krismer, E., Pedersen, A.-K., Pietzner, M., Olsen, J.V., Schoof, E.M., and Searle, B.C. (2023). Optimizing Linear Ion-Trap Data-Independent Acquisition toward Single-Cell Proteomics. Anal. Chem. 10.1021/acs.analchem.3c00842.

34.       Phlairaharn, T., Grégoire, S., Woltereck, L.R., Petrosius, V., Furtwängler, B., Searle, B.C., and Schoof, E.M. (2022). High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps. J. Proteome Res. 21, 2815–2826. 10.1021/acs.jproteome.2c00376.

35.       Bruker Daltonik (2023). 1901442-timstof-ultra-ebook-rev2.pdf. https://www.bruker.com/en/products-and-solutions/mass-spectrometry/timstof.html.