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After quantification I tried simulating
IDs in expression profile:
NM_001001130.3
IDs in reference:
\>NM_001001130.3 Mus musculus zinc finger protein 85 (Zfp85), mRNA
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### Description of feature
In the DDA/label-free workflow (perhaps in others as well), it would be useful to get an output of the identification results at the end of the search/inference/filtering p…
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31d09ecbdb8961c91070b9ce749b1c1c1c60071f fixes the omission of cis from the 'male' category such that the labels are now properly mutually exclusive. However, further improvements are desirable:
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DeMix-Q is a label-free quantification workflow that was recently published in MCP (http://www.mcponline.org/content/15/4/1467.full; shout-out to @hroest for pointing out the paper). It is largely bas…
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Greetings,
I am working on data analysis projects using OpenMS to search mass spectrometry data collected on a Fusion with a Thermo Fisher FAIMS device on the front end of the instrument.
We ha…
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Label-free quantification
Label-free quantification is a method that aims to determine the relative amount of proteins in two or more biological samples. It may be based on precursor signal intensity…
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Hi Vadim and team,
I have done 3 plex dimethyl labeling on samples and am now trying to analyze them following the steps outlined in the plexDIA section. But as you can see below, after finished wi…
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**Describe the bug**
Hello,
I am currently using MaxQuant for data analysis and have encountered an issue after updating from version 2.0.3.0 to 2.5.2.0. Previously, the Peptides.txt file used to …
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Dear Fragpipe team,
I am a beginner and am trying to follow the official label-free quantification tutorial to process the raw data obtained from the timsTOF pro 2. However, I did not get the expecte…
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The four issues below are related to the post-modelling treatment of EDS data, for quantification purposes.
1) after a model has been fitted, we use "result = m.get_lines_intensity()" to extract t…