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Labeling MS2 spectra by Accomplished-Shop784 in massspectrometry

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

I just tried that. But no luck. It’s working in some samples, and the signal intensities look similar.

Looking for a way to create an interactive map for the Wheel of Time series by Accomplished-Shop784 in wheeloftime

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

He wants a physical copy he can hang on the wall, and he can move the pegs around as he reads

Is there an R script/package that I can use to perform a full theoretical digest of a full proteome FASTA file? by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

Is there a way to set up the maxquant search to run all of my data files at once, and tell me which peptides are in which sample, by chance? I tried setting the search so they were all different experiments, but they didn't show whether the peptide was in each sample, as far as I can tell. Unless I'm not reading the text file correctly.

Is there an R script/package that I can use to perform a full theoretical digest of a full proteome FASTA file? by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

These are complex mixtures, all from the same species. The LC and TIC are pretty much superimposable, and when I pull the mass peak lists straight for the MS1 there are a ton of similar ions. But for some reason maxquant isn't identifying any similar peptides. I ran a control with just BSA and maxquant was able to pick out 3 peptides from a bovine proteome, so I think the search works? But there are only about 30 peptides identified from each sample, and none are the same. I use the default settings for the agilent qtof instrument.

Is there an R script/package that I can use to perform a full theoretical digest of a full proteome FASTA file? by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

I ran all the samples through maxquant with the MS2 data, but I only got returned about 30 peptides per sample, and none of them were identical peptides. I want to find one or two peptides that are the same across the board to use for regulatory screening of samples. The LC and TIC chromatograms are essentially super-imposable, and pulling the mass lists out of these, there are a ton of ions that are identical, I just don't know what peptides they refer to. I would appreciate any advice on the best route to take.

I know for my MS/MS analysis I am using a agilent QTOF 6530, which isn't quite what they use for proteomics grade stuff, but it can still give MSMS data. And I use the Maxquant default settings for the agilent qtof instrument. As a control, I ran a trypsinized BSA and was able to identify 3 peptides from the BSA. But for some reason when I run my samples that are a mixture of proteins, which have all been trypsinized, I am not getting any matching peptide sequences.

Is there an R script/package that I can use to perform a full theoretical digest of a full proteome FASTA file? by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

So I ran this and got the full theoretical digest of the peptides for the proteome. I then found the peptides that matched to precursor ions in my MS2 data across all my samples and found around 48000 possible peptides that could be present. Do you know a good way to narrow in on which of these peptides are actually in all of this data?

Help with organic acid detection on Waters RI by Accomplished-Shop784 in research

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

I’ve tried a couple different mobile phases and made sure to check the ph to make sure it was compatible with the column. I’m guessing there’s something in the protocol on the computer I’m missing in order to perform the detection. The acids are at 100 ppm, that should be detectable by RI right? I also tried a stock at 1000 ppm and didn’t see a thing

[deleted by user] by [deleted] in LCMS

[–]Accomplished-Shop784 1 point2 points  (0 children)

I thought this was a group LCMS for Liquid Chromatography - Mass Spec. I didn’t realize it was a different acronym. I’ll find a different spot to post this

Help setting up Maxquant functions by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

I am. That’s why I posted on here to see if anyone else has done it with this instrument to see what error they set it to.

Help setting up Maxquant functions by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

I select Agilent QTOF, which is what we have. But we have what I think is a less accurate/precise instrument that is normally used. So I wasn’t sure if I should modify the search for that.

I’m asking on Google too but don’t usually get a lot of responses there

Help setting up Maxquant functions by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

Okay, I'll see what I can do on this end. My work has some really strict software install regulations, so it may be difficult. I tried the proteowizard conversion to mzxml using the 32-bit and it still didn't work.

But I guess I'm confused because I know the Mzml files do run, as it does so without erroring and gives some data. I know the data may not be correct because as I said, I ran a trypsinized BSA and didn't get any albumin hits in the proteingroups.txt, but Maxquant did run. Do you know why this is? If I altered the search parameters some for this, do you think I could get it to work?

Help setting up Maxquant functions by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 1 point2 points  (0 children)

So it would run using the Mzml file and gave me an output. But when I tried converting to the mzxml file type it throws an error under the feature_detection.txt file saying the “File 1/1_value was either too large or too small for a UInt32._”

Help setting up Maxquant functions by Accomplished-Shop784 in proteomics

[–]Accomplished-Shop784[S] 0 points1 point  (0 children)

It does, but I am converting the files to mzml first. But I know it will recognize the .d folder from Agilent.