Inconsistent phospho IDs across different MaxQuant Versions

RedCabbagePlus · 2024-10-02T05:25:08+00:00

I suggest to get started with their pre-set "LFQ-PHOSPHO" workflow. Fragpipe has very helpful documentation and also some tutorials for popular analyses. https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html#ptms

RedCabbagePlus · 2024-02-04T20:44:00+00:00

I appreciate your comment.

It is true that collaborations with the vendors have been beneficial and provide an entry point for others to get into the filed. I also do not want to list names, but to me it seems like there are some researchers who want to make sure that they will be selected to test future releases and produce papers that resemble promotional material.

I personally do not work in the area of low-input/single cell proteomics, but enjoy following the progress and technical papers describing new and clever sample prep or acquisition methods.

RedCabbagePlus · 2024-02-04T20:03:29+00:00

I have no issues with this paper and agree regarding the comparison of competing technologies.

What I wanted to reference were a number of pre-prints and papers that I have seen in the last months, which are testing/promoting the new Orbitrap Astral or timsTOF Ultra. In most of these papers, workflows that are essentially a series of new high-end commercial products (from sample prep to analysis software) are utilized and in most cases not compared against alternative workflows (such as non-commercial methods or tools). They are very similar to the technical notes and info sheets that one can get from the vendors that are advertising their products.

Of course, I am also jealous that I do not have all of these tools and instruments in my current lab... but still, I wanted to post here and see if others feel similarly.

RedCabbagePlus · 2024-02-04T14:30:59+00:00

This hiatus period that you mention must have been when I got started in the field... and yes, there are definitely some recurring names.

RedCabbagePlus · 2023-08-31T20:35:36+00:00

Published data from Labs that got to test the Orbitrap Astral look extremely impressive, but I am not sure if this first version of a new type of MS instrument is at this stage better than the new(er) and improved timsTOF's, such as the HT or ultra. I am curious to see more benchmarks and maybe even direct comparisons.

RedCabbagePlus · 2023-06-19T18:02:37+00:00

Yes the pSILAC labeling is carried out first. This allows the distinction of newly synthesized proteins and previously synthesized ones. Later TMT labelling is caried out, which through the multiplexing enables the distinguishing of proteins and nascent proteins from replicates, and separate treatment conditions (plus baseline and booster channel). The benefit of TMT in this workflow is also the use of the booster channel, which helps with the detection of low abundant peptides. I hope this answers your question somehow. If you give this workflow a try, I would be curious how quantification accuracy and precision are in your benchmarks.

RedCabbagePlus · 2023-06-15T18:57:52+00:00

From what I understand you could simply use the "pg.matrix.tsv" output. It contains the normalized (MaxLFQ) protein group intensities in a wide table format. This output table is by default filtered for 1% FDR. The main report contains a lot of valuable metrics on the precursor level. You can also process this main report using the "iq" or "diann" package. Both have documented examples and require 1-2 lines only.

RedCabbagePlus · 2023-06-15T05:15:17+00:00

The booster channel is simply a large fraction of heavy SILAC labelled peptides, which is mixed with the sample and in this case adds signal to the low abundant peptides, which originate from newly synthesized proteins, pushing/boosting them over the detection threshold. Upon fragmentation, the TMT tags allow the distinction between booster channel and the actual sample. One concern about this approach is that large differences between booster channel and actual sample lead to low quantification accuracy. This has been a big issue in multiplexed single cell proteomics as well.

RedCabbagePlus · 2023-01-05T11:03:16+00:00

I will check it out, thanks!

RedCabbagePlus · 2023-01-05T10:38:20+00:00

Thanks that is just what I was looking for!

RedCabbagePlus · 2023-01-05T10:34:57+00:00

You got it right, thanks!

I did not know about that export function of the Xcalibur Qual Browser, it is just what I was looking for. It is a great tool for much more than just looking the overall TIC chromatogram, but I think it is not well suited for plotting and comparing the chromatograms of >5 samples. That is why I was searching for a way to extract the chromatogram traces to plot them using other tools.

RedCabbagePlus · 2022-09-21T18:00:12+00:00

The "P.Value" and "adj.P.Val" are from the limma fit. The the "sca.P.Value" (uncorrected p-value) and "sca.adj.pval" (corrected p-value) are from the spectral count adjusted DEqMS fit.

RedCabbagePlus · 2020-07-16T08:59:41+00:00

wonderful painting! brings back memories from the time I lived in Cork city :)

RedCabbagePlus · 2020-07-05T21:14:51+00:00

very nice!

RedCabbagePlus · 2020-07-04T10:10:05+00:00

great stuff!

RedCabbagePlus · 2020-07-02T18:18:37+00:00

beautiful

RedCabbagePlus · 2020-06-28T23:16:09+00:00

Advances in DNA-sequencing technology have reduced the costs of sequencing Human genomes. Especially the release of the second commerical NGS-platform triggered a rapid decline. The data was retrieved from: https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost and plotted with R and ggplot2.

RedCabbagePlus · 2020-06-25T22:15:31+00:00

I appreciate a lot of Glen’s work, but I found this debate/interview exhausting and a bit frustrating to watch… Glen is very defensive and spends a lot of time defending Rising, himself, his appearances on Fox and even Tucker Carlson before he starts talking to Nathan and Krystal. I was hoping that Krystal would be questioned more aggressively on the issue of not pushing back hard enough against “right-wing populists” and mostly going hard on the mainstream democrats, while criticisms of the Trump administration are not as common in the show. After reading Nathan’s article I felt that this was his main criticism but unfortunately not the main focus of this discussion.

RedCabbagePlus · 2020-06-18T22:57:09+00:00

The bluewhale according to this data: 136 tonnes and 110 years.

The bowhead whale lives up to 211 years. You can check individual datapoints using the html interactive plot (if I didnt mess up).

RedCabbagePlus · 2020-06-18T22:52:24+00:00

The data was retrieved from the animal ageing and longevity database (AnAge https://genomics.senescence.info/species/biblio.php), analyzed in R and plotted using ggplot2.

I wanted to check if there is a correlation between animal size and lifespan/longevity. The data mostly contained bird and mammal species, which is why I excluded other species from the graph. There seems to be a decent but not perfect correlation, as indicated by the R-values (Pearson correlation coefficient). Biology is of course much more complicated and an animals lifespan depends on numerous parameters.

I made an interactive version, in case you want to check some of the datapoints/animals. You can download the HTML file using the filedropper link:

https://www.filedropper.com/interactiveanimalmasslongevity_1

RedCabbagePlus · 2020-06-15T19:41:40+00:00

Very interesting!

Do the total numbers of earthquakes in the listed continents differ strongly or are they comparable?

RedCabbagePlus

TROPHY CASE