- by /u/Antique-Property-761How do you measure your peptide concentration after digest & clean up? I know Thermo sells their Fluoro and Colorimetric peptide measurement. They take so much sample and very often not accurate. submitted by /u/Antique-Property-761 [link] [comments]
- by /u/Practical-Buy-2439As I start to do lower and lower input proteomics, I'm concenred about losing peptide material to the walls of the 96-well plate in the autosampler. I was surprised to find very few low-protein bind options on the market. There are Eppendorf's deep-well low-protein-binding plates, but they well volume is huge compared to the 10uL I'll be putting them. Has anyone used the MicroResico low-protein binding plates from Amuza? https://www.amuzainc.com/shop/labwear/microresico-low-bind-96-well-plate/?srsltid=AfmBOoq9dDh_FvLrT-NWIZTA28fp1H0hHJg4vVlZd8fJl2tdCAcmQ65- What do the low input people use? submitted by /u/Practical-Buy-2439 [link] [comments]
- by /u/Antique-Property-761What's your injection load for a global BU proteomics – say with cell extracts? submitted by /u/Antique-Property-761 [link] [comments]
- by /u/JustsomegaaalIs it possible to normalise groups with quite different total intensities due to protein input not being standardised? More info: My experiment involves taking 30 mg of tissue to make conditioned media from tissue X and tissue Y. The protein concentration in conditioned media was too low to measure so we couldn't standardise the amount of protein loaded but used the same volume per sample. I want to do a differential analysis between the groups but because one tissue secreted a lot more than the other, this complicates things. Or does it? Pls help submitted by /u/Justsomegaaal [link] [comments]
- by /u/Deep-Comparison1242Hi, does anyone do SDS-PAGE analysis prior to digesting the lysate into peptides or do you just do quantitation? submitted by /u/Deep-Comparison1242 [link] [comments]
- by /u/hotsuninfreezingcoldDid go through Maxquant's on youtube but a book does help understand better. Am aware about online resources but is there no book for better understanding of the field? submitted by /u/hotsuninfreezingcold [link] [comments]
- by /u/SigmaGreaterHello all, I have a quick question regarding the differences between MaxQuant and FragPipe. I’m much more familiar with setting up experiments in FragPipe, but my PI has asked me to run the analysis in parallel using MaxQuant. The issue I’m running into is setting up my samples in MaxQuant. I have 15 raw files and I’m running TMT10. The 10 channels correspond to two groups: 5 control and 5 test, labeled 1–10, respectively. How should I label the groups and assign each sample to the correct channel in MaxQuant? I've looked up the problem a few times, but don't […]
- by /u/Arnubis94I'm having trouble with a spectral library generated in Peaks Studio. After DDA analysis, I generated a tsv file that I then wanted to use for SWATH DIA analysis in PeakView, but there seems to be a problem reading the file. Similarly, Spectronaut can't read the tsv file due to a different column format. Are there any viable ways to convert a tsv file from Peaks to PeakView format? Currently, the only thing I can do is generate mzidentml in Peaks and upload it to PeakView, but loading this file is a nightmare and takes literally days. submitted by /u/Arnubis94 […]
- by /u/budy_loveI typically just use tc18 cartridges from waters and haven't considered much else. However, lately I've been trying to optimize identifying peptides that are methylated on arginine (from cell lysates). These tryptic peptides often have multiple methylated arginines and I understand there has been success using strong cation exchange approaches or more hydrophilic SPE like HLB. I'm considering testing the oasis HLB SPE and I see there is an oasis MCX, which is a mix of RP and SCX I guess. Does anyone have experience with these or any useful tips/recommendations? submitted by /u/budy_love [link] [comments]
- by /u/RumbleStrut84Someone just opened up nice big containers of milk protein and BSA and weighed them next to me while I was prepping my buffers for proteomics sample prep. I found some clean, unused glassware and went to another clean lab to re-make everything. Normally I would not bother cleaning glassware for proteomics and just get new supplies, but I need to save money. Does anyone have a reliable method for cleaning glassware to remove protein contaminant? The containers would be used for making buffers to prep samples for proteomics so I am trying to avoid detergents. submitted by /u/RumbleStrut84 [link] […]
- by /u/Educational-Goal-736A question for the proteogenomics community here: I have been trying to create a custom protein database to identify variant peptides from DIA data downstream. So far, I tested both ProteoDisco (R) and pypgatk (python) without success. Do you have any suggestions for tools that I could use to create a custom protein database using a VCF file or a VEP annotated VCF containing variants of interest? Thanks! submitted by /u/Educational-Goal-736 [link] [comments]
- by /u/CommandOwn1557Hello, I would like to visualize all the entries in the FASTA I used for my proteomics search as a dataframe in R. Anyone know how to do this? submitted by /u/CommandOwn1557 [link] [comments]
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