- by /u/West_Camel_8577Is there a way to convert my PD3.1 output to the format used in MaxQuant STY sites files? PD output includes a modification sites file: PD modification Sites As well as the PSM, Peptide Groups, and Protein Groups files.. I really don't want to re-run this analysis on MaxQuant because I was able to use Chimerys and some other specific search steps in PD. But the downstream analysis programs I want to use (DEP2, PhosphoAnalyst, PhosMap, etc right now only take the PhosphoSTYsites.txt input submitted by /u/West_Camel_8577 [link] [comments]
- by /u/vintagelust0These are IP samples. I was not expecting the data to look like this? submitted by /u/vintagelust0 [link] [comments]
- by /u/Additional_Assist_18Hey guys. I am a PhD student who just got raw data back from an exploratory study in the form of label-free DIA. I have been recommended to process my files in Spectronaut. I have zero experience in bioinformatics/biostatistics and overall computation stuff, but keen to learn with this great opportunity/project. Can anyone advise what pipeline to follow and where can I find good resources to learn (literally) everything on how to go from raw files to visualisation graphs, please? How can I optimise all my stringency criteria during this pipeline? Any help will be greatly appreciated! 🙏 submitted by […]
- by /u/superblokesI am very new in Proteomics. Just wondering if anyone has a good book or review on Proteomics Analysis Plots like heat map, volcanos, how to use GSEA, etc. I know I can google these terms, but the output is overwhelming and I need to comb through them. Thank you submitted by /u/superblokes [link] [comments]
- by /u/No-Region-2187Does anyone have the experience in doing Micro BCA for total protein concentration before and after trypsin digestion. The buffer used before the digestion is PBS and the buffer is UA buffer after the digestion. The concentration of total protein increases up to 3 times after the digestion. Does Urea interferes? Also the conc. of urea is 20mM. Thank you submitted by /u/No-Region-2187 [link] [comments]
- by /u/DrymoglossumAn Open invitation to join mass spectrometry omics discord group mass spectrometry omics discord group submitted by /u/Drymoglossum [link] [comments]
- by /u/Simple_Carpenter_329Hi, I got Mass spec data in excel sheet. It is partially analysed, showing protein IDs, fold change, -log10 p value, number of peptides identified in each protein etc. I have 3 repeats of control and treated samples. What should i do next? I am doing basic analysis on Reactom by shortlisting significant up and down regulated proteins. What else I can do? I am new to this all and I would appreciate any step by step guidance. The purpose is to find the key pathways/targets affected by the treatment. Thanks submitted by /u/Simple_Carpenter_329 [link] [comments]
- by /u/No_Championship_5269I am using a self-filled column for single-cell proteomics (Astral+Vanqusih neo, 50 μm inner diameter, 1.5 μm C18, flow rate 250 nl/min, column temperature 55 degrees Celsius). When observing the tip of the column, I found a very obvious Taylor cone. How should I optimize my self-filled column? https://preview.redd.it/kar544mnqzce1.png?width=764&format=png&auto=webp&s=cc1cbda425096fdea5d9c3abe6266ca261e54006 submitted by /u/No_Championship_5269 [link] [comments]
- by /u/mai1595Our purchase dept requires us to do market research for the instruments we want to buy. We already gave them the unique selling points for the instruments but that was not enough. Do any of you have experience with market research for MS for Proteomics? Or could anyone give me an example document? Thanks for the help! submitted by /u/mai1595 [link] [comments]
- by /u/ElGranQuercusDoes anyone have experience that you could share related with formaldehyde-based crosslinking experiments? What concentration of formaldehyde and general procedure did you use? Any considerations when working with living cells? Did you take any special precautions when looking into the data after processing? Is there a particular published protocol that you would recommend? To give further information, I’m exploring a few possibilities to study a protein-protein interaction. Perhaps as expected, some of my formaldehyde tests have given me pretty much only garbage in return. Also looking into other crosslinkers like DSSO so if you can opine on that I would […]
- by /u/germetto0Hello guys! So, straight to the problem. I have a proteomics dataset in the form of a matrix, with 20 samples (as columns), and 6000 proteins (as rows). It's inside the picture inside this post. Protein expression is already log2 transformed. Performing a PCA with FactoMiner and Factoextra packages, with the following code: res.pca fviz_pca_var(res.pca) I obtain the PCA labeled 1 in the picture inside this post. By writing res.pca fviz_pca_var(res.pca) I obtain PCA 2 instead. Now, when I transpose the matrix, and by writing res.pca_t fviz_pca_ind(res.pca_t) I obtain PCA 3. Why do I have the difference in how the […]
- by /u/West_Camel_8577When comparing phosphorylation between a control and treated (paired data) what is the best way to go about this? Right now I am using TMTanalyst (Monash) and treat the phospho-enriched samples as a different 'condition' than the total proteome in the annotation file so that I can get expression graphs that show me the total protein quant (left) and the phosphoprotein quant (right). In the case of this example where there is only one phosphopeptide identified in this protein, the phosphoprotein quant boxplots technically only have quantification from that single phosphopeptide between the control and treatment. Given that I don't […]
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