What is the difference between FragPipe and DIA-NN?
Reddit - Proteomics
by /u/Drymoglossum
3d ago
I am familiar with DIA-NN. However I have been given a Linux HPC and not familiar with CL and unable to run DIA-NN since None of the Linux version comes with a GUI so its CL only. However I got to know FragPipe https://fragpipe.nesvilab.org/ in the apps available via Open OnDemand (OOD) which as DIA-NN as part of its pipeline and it comes with a GUI. ​ Is it possible to only use DIA-NN features from FragPipe? Anyone has a manual for this? submitted by /u/Drymoglossum [visit reddit] [comments ..read more
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Self-made ziptips?
Reddit - Proteomics
by /u/Worsaae
3d ago
My lab is out of c18 ziptips and I need about 20 tomorrow. However, we do have some c18-resin for preparing self-made stagetips. What would the difference be between commercial ziptips and if I made my own ziptips by placing one or two discs of c18-resin in the bottom of a 200 uL pipette tip? submitted by /u/Worsaae [visit reddit] [comments ..read more
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Is the structural comparison of 2 proteins a relevant way to detect protein-protein interactions (PPI) ?
Reddit - Proteomics
by /u/Owlyver
3d ago
I've read an article that structural similarity enhances interaction propensity of proteins. Does that mean we could (in theory) use tools like PDBeFold to do structural alignment of proteins and thus predict whether it is likely they will interact? A is similar to B => A in B are likely to interact. Normally when articles talk about structural similarity based approaches for finding PPIs, they use this assumption: "if two proteins A and B can interact with each other, then there may be two other proteins A′ and B′ whose structures are similar to those of proteins A and B; then it is impli ..read more
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Can you help me understand this study?
Reddit - Proteomics
by /u/themainheadcase
3d ago
There is a concern about the impact of antibiotics on male fertility, so this study looked into how various fertility parameters changed in the sperm of a young man taking H. pylori treatment. The methodology was as follows: A young man (23 years old) with Helicobacter pylori infection was treated with antibiotic therapy (amoxicillin 2 g/day for 15 days, clarithromycin 1 g/day for 15 days). During the medication (29 March–11 April 2022), semen samples were taken approximately every 3 days for a total of 5 times. After drug withdrawal (12–28 April 2022), semen samples were also taken approxim ..read more
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What is your favourite digestion technique? ?
Reddit - Proteomics
by /u/SC0O8Y2
5d ago
Just a fun question, do you have a favourite enzyme or chemcial for proteolytic digestion. If so why ? Do you have a cool story for it, or equally a bad experience that steered you away? My personal favourite is using hydroxylamine just because it seems cool. Honourable mention to lysarginase. submitted by /u/SC0O8Y2 [visit reddit] [comments ..read more
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Plotting PCA with DIA-NN and Spectronaut export files
Reddit - Proteomics
by /u/pepbro-
5d ago
I have just received the results of my data analysis in form of a summary excel sheet. However, I struggle to perform post analysis with python or R, mainly because I feel like a lot of data is missing. For example, in the spectronaut file I have information about the detected peptides and protein groups and can thereby calculate the number of identifications. But I have no intensity values (unless PG.quantity is another term for this?). Furthermore, I am not sure how much information I need to perform PCA since I am used to the software doing it automatically. I guess the question is, do I n ..read more
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Protein digestion
Reddit - Proteomics
by /u/Zesty_Pride_485
5d ago
I am just learning proteomics. I had one fundamental question. In one of the experiment where I digest a purified protein, I would like to use two proteases for protein digestion. I wonder why not these two protease don't chop each other decreasing the efficiency of target protein digestion. Even in single protease condition, won't it self cleavage? If you have a good reference article (protocol etc.) to understand rationale in each step would be helpful. Thanks! submitted by /u/Zesty_Pride_485 [visit reddit] [comments ..read more
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Proteome discoverer user guide
Reddit - Proteomics
by /u/Zesty_Pride_485
1w ago
Anyone have copy of Proteome discoverer 2.5 user guide? I could only get 2.2 but not 2.5. Thanks. submitted by /u/Zesty_Pride_485 [visit reddit] [comments ..read more
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What happened to the Plasma Proteome Database?
Reddit - Proteomics
by /u/bdubssbudb
1w ago
I was a prolific user of the Plasma Proteome Database back in grad school, but now the site appears nonfunctional. Not sure if this is temporary or permanent. I've emailed the authors of the original paper without any luck. Curious if anyone knows the back story on this, or has suggested alternatives? (The Human Protein Atlas is great, but it doesn't provide the comprehensive view of plasma concentrations that PPD did) submitted by /u/bdubssbudb [visit reddit] [comments ..read more
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Video for - Heat ‘n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour
Reddit - Proteomics
by /u/stevew91
1w ago
ProCan has published a paper outlining the sample prep method they have used for over 10 thousand cancer samples, the paper can be found here https://pubs.acs.org/doi/10.1021/acs.analchem.3c04708 While working there, I made a video outlining the lab process and have just uploaded it to YouTube, which can be found here: https://youtu.be/i2LGXr3Rfzw If anyone is interested in any of the 3D printed tools used in this video, the STL files can be found here: https://www.printables.com/@SteveW91/collections/139924 ​ submitted by /u/stevew91 [visit reddit] [comments ..read more
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