Tej

YouTube video by Brett Phinney Doing Differential Expression analysis on Proteomics Data using Limpa!!

Need to do some cutting edge Proteomics Differential expression? Maybe give Limpa a try! Guaranteed to rise to the occasion ...despite its name !

youtu.be/vqeOT8xcycc

Some new content at GitHub:

github.com/pwilmart/pow...

We have been measuring proteomes for a long time but almost never think about our data and results at the whole proteome level. We lose a lot of information when we think one protein at a time. We need to multiplex our thinking.

Are you having a LaPh? Diverse roles of Labile Phosphorylation in mammalian cells portlandpress.com/bi...

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#proteomics #prot-paper

"... if we're competitive from a price, thoughput and coverage perspective, the other technologies seem more than a bit silly. " That sums it up👍🏾

Enrichment of Cysteine S-palmitoylated peptides using Sodium Deoxycholate Acid Precipitation www.mcponline.org/ar...

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#proteomics #prot-paper

Struggling to compare Bruker timsTOF methods or extract window schemes from raw .d files? I developed a free desktop tool to solve this: timsCompare! 🚀

It automates the manual work of extracting method parameters, presenting them in a structured and comparable view.

(A thread 🧵)

Postdoctoral Fellow to study host-virus responses using proteomics and mass spectrometry stilling.forskning.n...

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#proteomics #prot-jobs

Twenty-Five Years of High-Throughput Screening of Biological Samples with Mass Spectrometry: Current Platforms and Emerging Methods Robust high-throughput screening (HTS) approaches for discovering new chemical entities are desirable for research and translation. Applications for which high-throughput (HT) methods are particularly...

Twenty-Five Years of High-Throughput Screening of Biological Samples with Mass Spectrometry: Current Platforms and Emerging Methods #AC pubs.acs.org/doi/10.1021/...

Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics www.biorxiv.org/cont...

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#proteomics #prot-preprint

PhD Position in Experimental Mass Spectrometry-Based Proteomics | JobTeaser www.jobteaser.com/fr...

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#proteomics #prot-jobs

Okay y’all. I’m at a complete loss. DIA is better on EVERYTHING on my Ultra2 except plasma digests. Neat, PC, PCA-N. DDA (pasef) works better. Coisolation FDR artifact? Anyone else see this?

PAMPA: A Software for Peptide Markers and Taxonomic Identification for ZooMS Samples in Archaeology and Paleontology pubs.acs.org/doi/abs...

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#proteomics #prot-paper

Mass Spec

Finally, we're looking for someone to join our #MassSpec Core Facility to support all the protein/peptide MS & development needs of our research groups utilising:

🧪Protein chemistry
📈Liquid chromatography
⚛️Tandem mass spectrometry
🖥️Data analysis

More at:
www.cruk.manchester.ac.uk/career/mi-25...

Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data - Nature Communications Mass spectrometry-based lipidomics and metabolomics generate large, complex datasets requiring effective analysis. Here, authors review key statistical and visualization methods alongside widely used R and Python tools, and provide a GitBook with step-by-step code for accessible, reproducible data analysis.

Best practices and tools in R and Python for statistical processing and visualization of lipidomics and metabolomics data #NatCommun www.nature.com/articles/s41...

91962-Research Technician, Proteomics Core | Memorial Sloan Kettering Cancer Center careers.mskcc.org/va...

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#proteomics #prot-jobs

YouTube video by CRUK Manchester Institute Group Leader Recruitment at the Cancer Research UK Manchester Institute

Exciting news - we are recruiting new Group Leaders! 🥼

We are seeking to appoint exceptional early-career scientists & clinician scientists as #GroupLeaders to develop bold, innovative, high-impact #CancerResearch programmes

Full details on our website: www.cruk.manchester.ac.uk/career/new-g...

Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs) Advances in mass spectrometry and associated computational tools have resulted in the wide-spread adoption of Data-Independent Acquisition (DIA) for proteomics. Experiments using state-of-the-art inst...

Are you using DIA mass spectrometry in proteomics?

We have just put this paper online: www.biorxiv.org/content/10.1...

Here, we came up with some Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)

1/4

Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High‐Throughput PRM‐MS in an Inflammatory Bowel Disease Cohort Validating biomarkers of disease is necessary for clinical use. The Health Surveillance Panel (83 peptides from 57 proteins) was developed as a PRM assay and evaluated using the Stellar-MS platform. ...

Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High‐Throughput PRM‐MS in an Inflammatory Bowel Disease Cohort #AngewChem onlinelibrary.wiley.com/doi/10.1002/...

‘Lipstick on a pig’: how to fight back against a peer-review bully Scientific societies, journals, editors and researchers are pushing back against mean-spirited peer reviews.

‘Lipstick on a pig’: how to fight back against a peer-review bully #Nature www.nature.com/articles/d41...

Final countdown! Only 3 days to go until the YPIC Webinar #19: Transition from Academia to Start-Up.

#YPIC #Proteomics #StartUpScience #ScienceCareers #AcademicToIndustry

Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...

#massspec #proteomics

Taking cue from ESCP25, tried the FAIMS std v low res and diff FAIMS voltages on Astral-Evosep zoom 80SPD using ionopticks Rapid 5x75 col. (DIANN2.0). CV -45V seemed to perform better for both 5ng and 250pg at precursor level. The story seemed a little different for CV-48V esp at lower 250pg conc..

[ASAP] Understanding Data Analysis Steps in Mass-Spectrometry-Based Proteomics Is Key to Transparent Reporting Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00287

(J Proteom Res) [ASAP] Understanding Data Analysis Steps in Mass-Spectrometry-Based Proteomics Is Key to Transparent Reporting: Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.5c00287 #MassSpecRSS

How to Apply Learn more about our application process

If you are interested in scientific software engineering or experimental work in the fields of spatial and multi-modal -omics, high throughput interaction proteomics, or mass instrumentation, apply until Oct 7th! @mannlab.bsky.social
www.biochem.mpg.de/mann
imprs-ml.mpg.de/How-to-Apply

'...higher number of proteins identified does not necessarily mean higher depth of soluble plasma proteome analysis...that higher number of proteins can be easily achieved in samples with background contamination, or tissue leakage due to organ failure...'

Final call: Applications close September 2! KI is recruiting 20 Assistant Professors in a wide range of subject areas. We're looking for early-career researchers with strong scientific merits and future potential. All positions: ki.se/en/about-ki/...

🚀 Release Day Alert! The brand-new #pmultiqc service is LIVE: www.ebi.ac.uk/pride/servic... 🎉 Instantly generate QC reports for #quantms, #DIANN, #MaxQuant & @pride-ebi.bsky.social datasets. Reviewing @pride-ebi.bsky.social quality data is super easy — all powered by pmultiqc: pmultiqc.quantms.org 🔥

The article here in, very well discusses the importance of randomisation, power analysis for designing meaningful experiments..there was also a JPR perspective on block randomisation for proteomics experiments..together make a nice primer..

pubs.acs.org/doi/10.1021/...

Public CPTAC Meeting dctd.cancer.gov/abou...

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#proteomics #prot-conf

From the reviewer's question, it seems to be for a niche application or atleast not conventional proteomics? Either way, access need not be investment limited ..core facilities come in handy here! Recently ours did nichePTM analysis upon client req 'with specific MS' as per their referred literature