- by /u/bluebottl3especially for targeted analysis since it can do 100+ proteins at abs quant? is the fusion protein the main limitation? Thought that with the advances in AI those can be solved for faster? submitted by /u/bluebottl3 [link] [comments]
- by /u/ApexDrifter_07Hi everyone I’m working on proteome-expression analysis for lung cancers (LUAD + LUSC) and trying to download the right files from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) / Proteomic Data Commons (PDC) portal. I’ve found the right study pages (e.g., for LUAD), but I’m stuck on: – identifying the correct processed proteome expression matrix (versus raw spectra etc), – finding the correct metadata/clinical file that aligns with it. If anyone has done this and can share exactly which file names (or a link) they downloaded for LUAD and LUSC, that would be super helpful. Also if you have any […]
- by /u/RendertheFatCapHey all, another question for the experts. As my lab is doing more proteomics, we're expanding to increase proteomic depth and coverage with high pH fractionation/concatenation. Is the typical Top3 method for protein LFQ quantification still valid under a fractionation/concatenation scenario? Or does the variable peptide recovery across 2 dimensions + any drying of fractions mean LFQ isn't possible? Can it be done, as long as each fraction is normalized to a similar injection volume/concentration? I've seen papers where people use heavy peptides for absolute quantification in plasma and a couple where the 2D fractionation/concatenation is used for LFQ with […]
- by /u/OmicsAndOmHey everyone, I’m trying to break apart very stable protein aggregates in preparation for mass spectrometry analysis. My goal right now is just to confirm that I’m getting enough protein and that the aggregates are actually being solubilized before moving on to MS. Following a couple of papers, I’ve been treating the aggregates with 90–100% formic acid for 1 hour at 37°C, then using a SpeedVac at room temperature for ~1 hour to dry and pellet the denatured proteins. The issue I’m running into is that when I try to measure protein concentration using a BCA assay, I don’t detect […]
- by /u/bluemooninvestorHi everyone, I am attempting to find interacting partners of a redox sensitive protein (contains cysteine active site) under control vs stressed condition? I expect quite a few of these interactions to be disulfide based. Normally, disulfide exchanges and oxidative changes are common during sample preparation steps. Can our experts share done tips on how to go about it? So far I have come across : 1) Use N-ethyl maleimide in lysis buffer. Why to use NEM when one can use IAA which is compatible with downstream alkylation step too? 2) Will NEM/IAA not interfere with antibody binding? More details […]
- by /u/Solid_Anxiety_4728There are so many version of human proteome. I am confuced. I spent hours trying to figure this out, and here's what I've gathered. But I still have two questions. Why they are so different in protein numbers. And do some of them contains single-amino acid polymorphisms (SAP). I am assuming not. ID protein_count Sequence redundancy additional uniprot UP000005640_9606 https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/ 20659 very low UP000005640_9606_additional (84851 proteins) emsembl GRCh38.pep.all https://ftp.ensembl.org/pub/release-115/fasta/homo_sapiens/pep/ 245535 high GRCh38.pep.abinitio (50174 proteins) NCBI GRCh38.p14 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/ 136807 high NCBI T2T-CHM13v2.0 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009914755.1/ 130470 high submitted by /u/Solid_Anxiety_4728 [link] [comments]
- by /u/Current-Juggernaut37https://proteomicsnews.blogspot.com/2025/10/maxquant-sdrf-enables-great.html submitted by /u/Current-Juggernaut37 [link] [comments]
- by /u/k2v2p2Hi everyone, I am fairly new to proteomics and currently optimizing mass spec for a biofluid sample that requires enrichment prior to the run. The sample is tricky from the start since it has very low overall protein concentration and limited protein diversity, but still contains some high-abundance proteins like albumin. I am trying to figure out how to choose the right instrument for this type of sample. How do you balance avoiding overload on a sensitive system while still injecting enough material to detect low-abundance proteins? Could someone weigh in on how to think about instrument selection in this […]
- by /u/Mona_SaintHello, I'm trying to analyze some label-free proteomics data, and I'm curious if there is a good way to gauge the relative abundance of specific proteins in the dataset. From what I understand, this can be done with spectral counting or peak intensity. My concern with peak intensity is the following: can't you have vastly different peak intensities even for two peptides that have the same true abundance? And also, intensity will vary by ionization state as well right? If so, then how can peak intensities practically be used? And then with spectral counting, what if you have peptides shared […]
- by /u/GugteyikkoI have a phosphoproteomics dataset with data at the level of phosphopeptides. Thus, some entries are annotated at multiple sites if they are on the same peptide, as in ADNP S953:S955. Unfortunately, it seems that some tools like Kinase Library's enrichment analysis require site-level annotation: it accepts peptide sequences centered on one phosphorylation site. Thus, it does not accept multiply-phosphorylated peptides, so I can't plug my data into it. Is there an accepted practice for collapsing my data to site-level annotations? Are there any tools available to do this, or will I need to write the code myself? If there's […]
- by /u/Fit-Purple324Hi people I ve been converting raw files to mzML with thermorawfileparser, tellling it to return me indexed mzML files. I noticed that the indexed files are huge compared to the non indexed, and their size is pretty close to the original raw files. So which one should i use for diann (v2+)? Thanks a lot for the help. submitted by /u/Fit-Purple324 [link] [comments]
- by /u/Plastic-Fan-6849Hi! So, I'm currently researching the protein contents in breadfruit (A. altilis), which there is not a lot of previous proteomic data on. I have run multiple jobs on FragPipe using jackfruit (A. heterophyllus) and breadnut (A. camansi) databases, and every single time I get keratin proteins?? Keratin is most definitely not found in breadfruit… I have no idea how to move forward to properly elucidate the identity of these keratin proteins. What should I try? Thanks!! submitted by /u/Plastic-Fan-6849 [link] [comments]
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