Keshava Datta, Ph.D.

One of the things that I find odd about academics is that even though they often have only had one job that their supervisor arranged for them, they talk about employment related matters with a confidence that one might assume was due to vast experience.

GitHub - pwilmart/quantitative_proteomics_comparison: Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies - pwilmart/quantitative_proteomics_comparison

DIA, DOA, DUI, DDA, etc. Here is a comparisons of some quantitative proteomics methods from a POV you might not have seen before:
github.com/pwilmart/qua...

Oh yes, the URL of the peptide mapper:
phbuffers.org/Claude/pepti...

High throughput single-cell proteomics of in vivo cells Single-cell mass spectrometry-based proteomics (SCP) can resolve cellular heterogeneity in complex biological systems and provide a system-level view of the proteome of each cell. Major advancements i...

High throughput single-cell proteomics of in vivo cells #MCP #MassSpec www.mcponline.org/article/S153...

"More" IS "Better", no?
(\sarcasm)

Enhancing Sensitivity in Low-Load Proteomics Orbitrap Workflows via SLIM Integration A Structures for Lossless Ion Manipulation-Orbitrap Exploris 480 (SLIM-OE) ion mobility mass spectrometry (IM-MS) platform was developed, integrating SLIM IM separation with Orbitrap MS analysis. A “s...

Enhancing Sensitivity in Low-Load Proteomics Orbitrap Workflows via SLIM Integration #AC pubs.acs.org/doi/10.1021/...

Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer Mass spectrometry based targeted proteomics methods provide a sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semistochastic sampling, or empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of the peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer’s disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits a quantitative precision similar to that of published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional upfront data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same data set.

Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer #JProteomeRes pubs.acs.org/doi/10.1021/...

High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria Systematic mapping of protein-ligand interactions is essential for understanding biological processes and drug mechanisms. Peptide-centric local stability assay (PELSA) is a powerful tool for detectin...

Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...

🤣

Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort. Despite advances in clinical proteomics, translating protein biomarker discoveries into clinical use remains challenging due to the technical complexity of the validation process. Targeted MS-based proteomics approaches such as parallel reaction monitoring (PRM) offer sensitive and specific assays for biomarker translation. In this study, we developed a multiplex PRM assay using the Stellar mass spectrometry platform to quantify 57 plasma proteins, including 21 FDA-approved proteins. Loading curves (11-points) were performed at 4 sample throughputs (100, 144, 180, and 300 samples per day) using independent, optimized, and scheduled PRM methods. Following optimization, an inflammatory bowel disease (IBD) cohort of plasma samples (493 IBD, 509 matched controls) was analyzed at a throughput of 180 SPD. To monitor system performance, the study also included 1,000 additional injections for system suitability tests, low-, middle-, and high-quality controls, washes, and blanks. Using this approach, we observed high quantifiability (linearity, sensitivity, reproducibility) in the PRM assay and consistent in data acquisition across a large cohort. We also validated the candidate IBD markers, C-reactive protein and orosomucoid protein, identified in a recent discovery experiment.

(BioRxiv All) Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort.: Despite advances in clinical proteomics, translating protein biomarker discoveries into clinical use… #BioRxiv #MassSpecRSS

Don't think it's relevant but "praja" in Sanskrit means "citizen" 🤣

Missed writing "non-redundant" tryptic peptides

Interesting. I wonder what this would look like if the cutoff scores were plotted against # tryptic peptides rather than # of entries in the FASTA.

Significant impact of consumable material and buffer composition for low-cell number proteomic sample preparation chemrxiv.org/engage/...

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#proteomics #prot-preprint

Toward Real-Time Proteomics: Blood to Biomarker Quantitation in under One Hour Multistep multihour tryptic proteolysis has limited the utility of bottom-up proteomics for cases that require immediate quantitative information. The power of proteomics to quantify biomarkers of health status cannot practically assist in clinical care if the dynamics of disease outpaces the turnaround of analysis. The recently available hyperthermoacidic archaeal (HTA) protease “Krakatoa” digests samples in a single 5 to 30 min step at pH 3 and >80 °C in conditions that disrupt most cells and tissues, denature proteins, and block disulfide reformation thereby dramatically expediting and simplifying sample preparation. The combination of quick single-step proteolysis with high-throughput dual-trapping single analytical column (DTSC) liquid chromatography–mass spectrometry (LC–MS) returns actionable data in less than 1 h from collection of unprocessed biofluid. The systematic evaluation of this methodology finds that over 160 proteins are quantified in less than 1 h from 1 μL of whole blood. Furthermore, labile Angiotensin I and II bioactive peptides along with a panel of protein species can be measured at 8 min intervals with a 20 min initial lag using targeted MS. With these methods, we analyzed serum and plasma from 53 individuals and quantified Angiotensin I and II and over 150 proteins including at least 46 that were not detected with trypsin. We discuss some of the implications of real-time proteomics including the immediate potential to advance several clinical and research applications.

Awesome paper, where we present and evaluate the methodology that will someday enable real-time monitoring of circulating biomarkers. pubs.acs.org/doi/full/10....

In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics pubs.acs.org/doi/ful...

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#proteomics #prot-paper

A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness molecular genetics, classification of proteins, methodology in biological sciences, cancer, and cell biology

It feels a little bit postclimactic to post this now, after the first version of our paper hit bioRxiv when X was still a thing that people used, the revised version was formally accepted at Cell Community past November. But here is the final print version of our paper

www.cell.com/iscience/ful...

Introducing Gaia: Context-Aware Protein Search Across Genomic Datasets — Tatta Bio Gaia is an embedding-based search engine for sequences.

Have a protein of unknown function? Try this www.tatta.bio/blog/gaia ! This is imo one of the best ai tools I have seen since alphafold alpha fold. I recommend you look at the paper too! #bioinformatics #biologicalDarkMatter #Gaia #tatta

(BioRxiv All) PepCentric Enables Fast Repository-Scale Proteogenomics Searches: Identifying novel peptides arising from alternative splicing, mutations, or non-canonical translations is a crucial yet challenging aspect of proteogenomics. We introduce… http://dlvr.it/TJFswF #BioRxiv #MassSpecRSS

Enhancing tandem MS sensitivity and peptide identification via ion pre-accumulation in an Orbitrap mass spectrometer www.biorxiv.org/cont...

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#proteomics #prot-preprint

The Current Landscape of Plasma Proteomics: Technical Advances, Biological Insights, and Biomarker Discovery www.biorxiv.org/cont...

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#proteomics #prot-preprint

Proteomics Scientist | John Innes Centre The John Innes Centre (JIC) seeks a talented, motivated individual as a proteomics specialist to serve the growing needs of proteomics-based technology at JIC, which is a globally recognized…

VACANCY - We’re seeking a Proteomics Scientist to work alongside our experienced platform manager to help serve the growing needs of proteomics-based technology at the John Innes Centre (JIC).

www.jic.ac.uk/vacancies/pr...

Closing date - 2 March 2025
Contract - Full-time, indefinite

Identifying receptor kinase substrates using an 8,000 peptide kinase client library enriched for conserved phosphorylation sites In eukaryotic organisms, protein kinases regulate diverse protein activities and signaling pathways through phosphorylation of specific protein substrates. Isolating and characterizing kinase substrat...

Identifying receptor kinase substrates using an 8,000 peptide kinase client library enriched for conserved phosphorylation sites #MCP #MassSpec www.mcponline.org/article/S153...

(ABioanChem) Quantitative proteome-wide O-glycoproteomics analysis with FragPipe: Abstract




Identification of O-glycopeptides from tandem mass spectrometry data is complicated by the near complete dissociation of O-glycans from the peptide during collisional… http://dlvr.it/THhR43 #MassSpecRSS

Interesting discussion! 🌟 For those interested in performing multi-omics integration with proteomics, transcriptomics, and metabolomics datasets, check out TurbOmics! 🚀. It's a user-friendly web-based platform including multivariate models such as MOFA and MBPLS: proteomics.cnic.es/TurboPutativ...

Do you want to explore the PTMs you identified in your last MS experiment in a fun, interactive way? Try it out on our PTMVision web server at ptmvision-tuevis.cs.uni-tuebingen.de and check out the new publication in JPR at doi.org/10.1021/acs....!

Nice! 🔖 Bookmarking for my future reference..

Characterization of 53 Multiplexed Targeted Proteomics Assays for Verification Studies in Cancer Cell Lines The National Cancer Institute’s Clinical Proteomics Tumor Analysis Consortium (CPTAC) was established to address the need for improved design, standardization, and validation of proteomics assays to enable better translation of biomarkers from the analytical lab to the clinic. Here, we applied CPTAC guidelines to characterize quantitative mass spectrometry (MS) assays in a new multiple reaction monitoring (MRM) proteomics panel. The panel of 50 proteins was developed in response to a previous study that identified a proteomic profile of altered translational control associated with response to a new cancer drug. MRM-MS assays for 53 peptides of interest were developed, optimized, and characterized on a UPLC system coupled to a triple-quadrupole mass spectrometer (QQQ-MS) using synthetic proteotypic peptides and corresponding stable-isotope labeled internal standard (SIS) peptides. Most of the assays were found to be fit-for-purpose for biomarker verification in that they precisely and reproducibly quantify the peptides at levels corresponding to the endogenous concentration in the desired cancer cell lines. Of these, 28 peptide assays represent to proteins that previously had no associated assays published in the CPTAC database. The targeted proteins in this publicly deposited validated multiplexed panel may be of use for research applications in cancer, cellular stress, neurology, cardiology, and metabolism.

Characterization of 53 Multiplexed Targeted Proteomics Assays for Verification Studies in Cancer Cell Lines #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

The cover image portrays a human composed of proteins who is examining their health status (represented by the ECG monitoring interface) with the assistance of artificial intelligence (represented by the chip and binary codes).

Something you don't see every day!
Digitizing the human proteome in >53,000 individuals with 15-year follow-up and, with machine learning, unraveling nearly 500 disease-causing proteins
www.cell.com/cell/fulltex...
open-access

Favorite figure showing how poorly RNA and protein correlate?