How to ruin an expensive experiment: "Cellular proteins were harvested from three biological replicates at each condition, and the proteins were pooled into one sample for further sample preparation."
Alison Chaves
@alisonchaves.bsky.social
Doing proteomics until I still can. https://github.com/41ison
As far as I can tell, I just received the best peer-review criticism of my life. Real improvement suggestions. Things I wasn't aware of when making some decisions. I couldn't be happier. This is a sincere thanks to reviewers.
Our latest work is out in Protein Science. Check the effects of B. jararaca (snake) envenomation in plasma. onlinelibrary.wiley.com/share/M2WGBJ...
Systemic impact of intramuscular snake envenomation and intravenous immunoglobulin‐based antivenom treatment on murine plasma proteome and peptidome
Reader environment loaded
onlinelibrary.wiley.com
Expectations in de novo search field: 1. Cascadia working; 2. Casanovo reporting RT and making non-tryptic ckpt compatible with the last release; 3. InstaNovo with winnow integrated; 4. GUI for InstaNovo; 5. Fragnovo release in FragPipe; 6. this is one interesting: langtaosha.org.cn/lts/en/prepr...
Accurate and ultra-fast de novo HLA-I immunopeptide sequencing with FoxNovo
We present FoxNovo, a hybrid deep learning-combinatorial framework for de novo sequencing of immunopeptides trained on a large-scale HLA-I immunopeptidomics dataset assembled and reprocessed from publ
langtaosha.org.cn
If you are a reviewer, please don't request that the authors cite your work. When the field is niche, we know who you are!
I don't know if Professor Hamkins is on bsky, but you definitely need to watch his lectures available on YouTube.https://www.youtube.com/watch?v=4Y9p0yp8Mow
Zeno's Paradox and Infinite Sums — Lectures on Infinity (Lecture 1)
YouTube video by Ergo
youtube.com
If you work in the field of medical mycology, I have a review article to share with you. It’s from 2021, but still worth reading. doi.org/10.1080/1040...
What is the elephant in the room when considering new therapies for fungal diseases?
The global scenario of antimicrobial resistance is alarming, and the development of new drugs has not appeared to make substantial progress. The constraints on drug discovery are due to difficultie...
doi.org
N-Terminal Coumarin Derivatization-Aided De Novo Peptide Sequencing and Its Application to Peptidomics Using LC-Trapped Ion Mobility Spectrometry-qTOF/MS | Analytical Chemistry pubs.acs.org/doi/10.1021/...
N-Terminal Coumarin Derivatization-Aided De Novo Peptide Sequencing and Its Application to Peptidomics Using LC-Trapped Ion Mobility Spectrometry-qTOF/MS
De novo peptide sequencing using LC–MS/MS enables database-independent sequence determination and facilitates the discovery of bioactive peptides and biomarkers in untargeted peptidomics. However, conventional MS/MS analyses often produce fragment ions that are insufficient for complete sequencing. Here, we established an LC–MS/MS workflow using N-succinimidyl 7-methoxycoumarin-3-carboxylate (Me-Cou) as an N-terminal tag to improve de novo sequencing performance. Me-Cou derivatization generated highly informative fragment ions, particularly b1–b3 ions, for (Gly)4 at 1 μmol/L, surpassing the performance of established tags, such as 2,4,6-trinitrobenzenesulfonic acid, 3-aminopyridyl-hydroxy-succinimidyl carbamate, and N-succinimidyl [tris(2,4,6-trimethoxyphenyl)phosphonio]acetate bromide. The Me-Cou tag also enabled confident sequencing of (Gly)10, generating abundant b1–b9 ions. Notably, intact de novo sequencing identified 74 peptides with 32 misidentified peptides that were not included in a 132-standard peptide mixture (86 dipeptides and 46 oligopeptides). However, all peptides were correctly identified using Me-Cou-aided de novo sequencing with no misidentification, demonstrating high specificity and accuracy. Additionally, Me-Cou-aided de novo sequencing successfully identified 328 peptides in casein peptone, all of which were assigned as casein protein fragments. Overall, Me-Cou-based LC–MS/MS significantly enhanced peptide detection and the characterization of sequence diversity compared with intact analysis. This methodology is a promising strategy for untargeted peptidomics, enabling comprehensive characterization of endogenous peptides in both protein hydrolysates and biological fluids.
pubs.acs.org
If you are looking for an easy way to compute iBAQ from DIA-NN output, ibaq4diann R package is for you. Try it out at: github.com/41ison/ibaq4...
"Under identical conditions, signals corresponding to 20 proteinogenic amino acids, 4 post-translationally modified amino acids, 32 peptides, 6 modified peptides, 11 bioactive peptides and 2 neoantigen peptides were recorded." www.nature.com/articles/s41...
High-resolution nanopore peptide sensing, profiling and sequence assembly - Nature Nanotechnology
A nickel-modified nanopore enables simultaneous, unambiguous identification of amino acids and peptides. Direct analysis or hydrolysis-based sequencing can be used for profiling and reconstruction, an...
nature.com
The following fragment of code if from fragpipe de novo. Does that mean that de novo in fragpipe will run DIA? private static final String[] MODEL_OPTIONS = { "DDA_MassIVE", "ddaPASEF", "DIA_Orbitrap", "diaPASEF", "nonspecific" }
What if all the PIs who ordered antibodies from Thermo on Zenodo's list asked for a refund? 🤔
Reese Richardson@reeserichardson.bsky.social · 2mo agoThe Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
A great study from Medzhitov's Lab 👏 Heme orchestrates a tissue stress response to proteolytic damage "our studies provide a mechanistic bridge between proteolytic injury and NRF2 activation." www.biorxiv.org/content/10.6...
biorxiv.org
The case against the Excel for data analysis! A summary from 2004 to 2022.
One more for the people asking "Where is the WB validation?" in proteomics. And Juvenal, the poet, not your cousin, reflects: Who watches the watchmen?
Sholto David@sholtodavid.bsky.social · 3mo agoSurprised to discover that Thermo Fisher appears to show a fake western blot for the validation of one of their p53 antibodies. I've added a diagram to show the very similar bands. This does not appear to be one of the "published figures" but their own internal data.
I had a great time in Ponta Grossa (PR) city at I Escola Integrada de Ciências Ômicas dos Campos Gerais. Lovely town, great university (UEPG), and new friends. Thanks for having me there.
This is a place to feed the brain. Thanks Dr. Nikolai Slavov for sharing this with us. blog.slavovlab.net/2025/08/16/p...
Proteins made to die
Protein synthesis is among the most energy-demanding processes in a cell. Yet, some proteins are synthesized and immediately degraded. This may seem like a futile cycle, but it’s a remarkable…
blog.slavovlab.net
"This discovery calls into question the textbook purple-or-pink dichotomy, decoupling stain color from membrane architecture." www.nature.com/articles/s42...
Gram-negative-staining Bacillaceae with thick cell wall and monoderm architecture uncover evolutionary diversity and challenge Gram-based classification - Communications Biology
Genomic and microscopy evidence shows that the Bacillaceae, assumed to only stain Gram-positive, actually have some lineages staining Gram-negative, yet unexpectedly maintaining a thick wall and no ou...
nature.com
First impressions on Uniprot changes in proteome fasta header. I don't like it.
A harsh truth about developers in the de novo proteomics field: they don't care about user experience. Do you know why Windows (~60%) and macOS (~15%) are more popular than Linux (3%) in the desktop computer world? Because they care about user experience!
Is there a file generated by FragPipe that stores information similar to the msms.txt file from MaxQuant? That is, matches (b and y ions), intensities, and m/z values. If not, adding this information would be invaluable. #FragPipe
Intrusive thought of the day: a proteomics publication using DIA-BERT to investigate a cohort of individuals with diabetes. www.nature.com/articles/s41...
DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis - Nature Communications
Data-independent acquisition mass spectrometry (DIA-MS) has emerged as a key technology in quantitative proteomics. Here, the authors introduce DIA-BERT, a transformer model pre-trained on existing DI...
nature.com
People doing de novo proteomics. Did anyone test this idea of open search for de novo search? I'm planning to play with it and report some toy dataset here in the next few days. github.com/pFindStudio/...
GitHub - pFindStudio/pUniFind: Official repo for pUniFind, the first open de novo sequencing and open database search rescoring deep learning model.
Official repo for pUniFind, the first open de novo sequencing and open database search rescoring deep learning model. - pFindStudio/pUniFind
github.com
A nature-inspired ion trap for parallel manipulation of ions on a massive scale www.science.org/doi/... --- #proteomics #prot-paper
DIANN users: making your life easier when evaluating your DIANN search results. QC4DIANN_v1.1.0 has new visualizations and now accepts the fasta you used to generate the speclib as a reference for calculating the proportion of proteotypic peptides per sample. Release 👉 github.com/41ison/QC4DI...
FragPipe users: I've updated PSManalyst shiny app. Check it out and enjoy the easiest way to evaluate the quality of your runs. Now you can map peptides to protein coverage counting PSMs. github.com/41ison/PSMan...
