/r/proteomics/

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  • Chimerys Errors in PD
    by /u/West_Camel_8577
    like the title says- I am using Chimerys in PD, and getting errors. I have tried 30+ times with different settings and inputs and haven't gotten it to work once so I'm considering giving up on it because it just prolongs the processing time and there is no manual or description of the error codes anywhere. Anyway here are the 3 errors I consistently get some combination of: (1) All charge groups contain less than 100 candidates which is the minimum requirement per group for CE calibration. Please revisit the combination of raw file, fasta file, and search settings. (2) […]
  • ny opinions on Alamar's Argo HT system?
    by /u/seqinsight
    Does anyone have any experience with Alamar's Argo HT system? How is the workflow and what assays did you use? How do you compare with Olink and Somalogic? submitted by /u/seqinsight [link] [comments]
  • Negative Intensity Values after log2 transformation (MaxQuant/Perseus/TMT)
    by /u/West_Camel_8577
    In perseus I filtered my matrix to exclude potential contaminants, decoy sequences, and proteins only identified by site. I then log2 transformed the intensity values and they are now all negative numbers. I am not sure if the normalization modes I set in MaxQuant (v2.6.7.0) mean that I shouldn't normalize my data in this way (I was using the Reporter_Intensity columns, not the "corrected" or "counts" reporter intensity) My MaxQuant settings are: TYPE: Reporter MS2, I have entered the correction values for my batch of TMT 10-plex, Filter by PIF is selected -> Min. reporter PIF 0.6 Min. base peak […]
  • OpenMS issue
    by /u/Logical-Composer9928
    Anybody using OpenMS here? I'm having a couple of issues while running the "FeatureFinderCentroided" program in OpenMS. I'm trying to run "FeatureFinderCentroided" to find lc-ms features, from some of the already centroided (by Proteowizard/MS-Convert, PeakPicking == True) mzML files, using the following command. My samples are C13 labeled FeatureFinderCentroided -in S4.mzML \ -out features_S4.featureXML \ -threads 36 \ -mass_trace:mz_tolerance 0.004 \ -isotopic_pattern:mz_tolerance 0.005 \ -isotopic_pattern:abundance_12C 86.56 However if there are any of the following three params, the program will not run -mass_trace:mz_tolerance 0.004 \ -isotopic_pattern:mz_tolerance 0.005 \ -isotopic_pattern:abundance_12C 86.56 Complaining that "Unknown option(s) '[-isotopic_pattern:abundance_12C]' given. Aborting!" etc. Am I missing […]
  • TMT and PTM analysis
    by /u/fallo92
    Hi all, I’m looking to get some ptm-level comparisons out of some datasets, mainly this paper where the authors looked at relative abundance (multi batch TMT6) of proteins across age groups in skeletal muscle. I was thinking of going deeper and seeing if there are differences at the ptm level across age. Before I spend a fun weekend reanalysing their 300+ raw files, an issue occurred to me that if the samples were TMT labelled, does this rule out any sensible ptm analysis for say ubiquitination or acetylation of lysines? Only the unmodified free lysines would get a TMT label, […]
  • Quantifying proteins based on 1 peptide – is it ever justified?
    by /u/gold-soundz9
    I understand that 2 peptides is the best practice, but that can result in a "loss" of up tp ~25% of proteins. Is there ever a good reason to use 1 instead of 2+? Packages like DEqMS are supposed to account for this variance by downweighing proteins quantified with 1 peptide, but does that totally solve the problem? I'm particularly curious about this in downstream analysis where some packages offer flexible algorithms for using 1 or 2 peptides to quantify proteins. DEqMS pub link, for anyone interested: https://pmc.ncbi.nlm.nih.gov/articles/PMC7261819/ submitted by /u/gold-soundz9 [link] [comments]
  • Is it worth doing DIA on Q Exactive Plus? Or DDA is better. For LFQ plasma proteomics.
    by /u/bluemooninvestor
    Please suggest both for depeletd and undepleted samples. I guess DIA is better for undepleted sample, but is Q Exactive plus capable enough anyway? submitted by /u/bluemooninvestor [link] [comments]
  • Are there any publications which compares different protocols for plasma/serum proteomics?
    by /u/bluemooninvestor
    There any many for general bottom up proteomics. But I couldn't find any for plasma proteomics, which would involve some differences I presume. submitted by /u/bluemooninvestor [link] [comments]
  • Bad data?
    by /u/vintagelust0
    Hi all, I ran two samples on mass spec. While analyzing them on scaffold, the identified protein is submitted by
  • MaxQuant Error Writing Tables
    by /u/West_Camel_8577
    Hi all, I am getting the following error when running MaxQuant- id0 start13/12/2024 21:18:06 titleWriting_tables (001/131) description\\CSM-CAB-MASSNAS\Data\1Talia\240112_CmRP8_TMT\combined\proc Writing_tables 0 Writing_tables (001/131) Process 23 0 \\CSM-CAB-MASSNAS\Data\1Talia\240112_CmRP8_TMT\combined \\CSM-CAB-MASSNAS\Data\1Talia\240112_CmRP8_TMT\mqpar.xml False 0 error\\CSM-CAB-MASSNAS\Data\1Talia\240112_CmRP8_TMT\combined\proc Writing_tables 0 Writing_tables (001/131) Process 23 0 \\CSM-CAB-MASSNAS\Data\1Talia\240112_CmRP8_TMT\combined \\CSM-CAB-MASSNAS\Data\1Talia\240112_CmRP8_TMT\mqpar.xml False 0_The process cannot access the file '\\CSM-CAB-MASSNAS\Data\1Talia\240112_CmRP8_TMT\combined\ser\proteinGroups.ser' because it is being used by another process._ at Microsoft.Win32.SafeHandles.SafeFileHandle.CreateFile(String fullPath, FileMode mode, FileAccess access, FileShare share, FileOptions options)__ at Microsoft.Win32.SafeHandles.SafeFileHandle.Open(String fullPath, FileMode mode, FileAccess access, FileShare share, FileOptions options, Int64 preallocationSize, Nullable`1 unixCreateMode)__ at System.IO.Strategies.OSFileStreamStrategy..ctor(String path, FileMode mode, FileAccess access, FileShare share, FileOptions options, Int64 preallocationSize, Nullable`1 unixCreateMode)__ at System.IO.Strategies.FileStreamHelpers.ChooseStrategyCore(String path, FileMode mode, […]
  • Can I find (old) raw data somewhere to use for practice?
    by /u/Aphanizomenon
    Hi, I'm looking in getting into proteomics and right now I am learning by myself from internet resources. I want to learn the Max Quant program, with the help of their summer school and guidelines on the internet, but it would be really helpful if I had some actual data to practice on. Does anyone know if there are raw files published somewhere on the internet? Alternatively, would anyone be willing to send me files from old/already used for publishing raw files or something you won't use? Thank you so much in advance and sorry if the answer is obvious, […]
  • Has anyone succesfully transitioned from lab to mass spec core facility specially in leadership position. Looking to make a transition after 8 years of postdoc. It would be great to connect and any advice is much appriciated.
    by /u/2Diamond_Hand
    submitted by /u/2Diamond_Hand [link] [comments]

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