5
votes
Accepted
How to interpret PCA output statistically and biologically?
All that plots like this are telling you is that there are some genes that contribute more to the variability seen between your various samples than others. In an ideal world these genes will also be ...
- 19.6k
4
votes
Accepted
Running MaxQuant on Linux
There is a conda package for maxquant that should work on most platforms (I've used it on CentOS and I think it's been used on Ubuntu as well). There's also a docker container version of that that we (...
- 19.6k
3
votes
Preparing PDB file for modeling with Swiss-Model
As explained in the website the data introduced must be:
Format must be FASTA, Clustal, plain string, or a valid UniProtKB AC
So you need to paste just the protein sequence. Without seeing the ...
- 4,693
3
votes
Omics data: How to interpret heatmap and dendrogram output?
You may be interested in reading up on heatmaps. For a history perspective (pre the biological introduction by Eisen et al. ) read The History of the Cluster Heat Map by Wilkinson and Friendly
- 31
3
votes
Accepted
Omics data: How to interpret heatmap and dendrogram output?
The dendrogram summarize the information of a group of values and sort them according to the similarity they have. It can be applied to both, samples and features.
The dendrogram allows to visualize ...
- 4,693
2
votes
Accepted
Principle of TMT Tags in Multiplex Proteomics
TMT stands for tandem-mass-tag. The idea is to tag different samples with one of the tags then pool all samples together and run them through the mass spectrometer together. Then the reporter groups ...
- 1,295
2
votes
Accepted
How I normalize these two sets of data
There's no need to normalize them, you're not comparing them. Just use them as they are.
- 19.6k
2
votes
What is the purpose of 'Folder locations' in MaxQuant?
These folders are usually generated in a default directory (where the raw files are). It can however be beneficial to set the paths to these folders manually.
Temporary folder
that is obviously ...
- 121
2
votes
Running MaxQuant on Linux
I have been running MaxQuant quite frequently on Linux. I would use conda to create a dedicated environment and install mono.
...
- 1,295
2
votes
Mapping protein refseq to Gene ID
You can do this with the reutils package, which provides an API to NCBI's E-utilities. Here's an example for your specific question:
...
2
votes
Accepted
median normalization for proteomics
The kind of normalization depends on what you what to explore. So, there is no absolute answer to this. Different normalizations highlight different aspects of your dataset. There is a nice paper for ...
- 1,295
2
votes
How can I match sequences with IDs using python dictionaries?
Biopython can index a fastafile and you can access the sequences by their ID in a dict-like manner.
All that is left for you to do is extract the IDs from your file. (more Biopython)
- 653
2
votes
Accepted
Peptide data visualization
The length of the bars and their placement on the x-axis represents the length of the peptide and mapping to the source protein, respectively. The coloring represents the average difference in peptide ...
- 36
2
votes
How identifiable are human omics data and how to mitigate their identifying features?
This is one of the major problems with genomic information in todays research. This was highlighted some years ago with the police using publicly available genomic data bases to idenitfy unkown murder ...
- 876
2
votes
De novo antibody sequencing fromMS/MS Ion Trap proteomics raw signal
A few notes on data generation first:
There are currently two broad approaches for the generation of bottom-up or "shotgun" MS proteomics: data-dependent acquisition (DDA) and data-...
2
votes
Gene/protein expression specific to a group in omics
You can never be 100% sure that a difference is real and not a statistical fluke. This is the entire concept underlying Type I errors - these are errors where the null hypothesis (usually, that there ...
- 246
2
votes
To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?
There is no direct support for this by best knowledge. Similar questions have been asked previously in the Bioconductor support forum, for example:
https://support.bioconductor.org/p/64300/#64793
They ...
- 1,108
1
vote
Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?
Small samples size and parametric tests are not mutually exclusive. Specialized software has been developed to leverage sharing information across measurements to boost power, that is called ...
- 11
1
vote
Accepted
Reduce Overfit by removing insignificant proteins through PSEA analysis
Overfitting is usually resolved by adding more data and not removing data sets. The technical blurb is 'augmenting' your training data set to revolve overfitting.
It is possible there is a very large ...
M__♦
- 11.9k
1
vote
Convert Mascot mztab file format to XML
There are a number of converters to be found at http://www.pastelbioscience.co.uk/resources/databases.html , although not sure that the one you are looking for is among them. May also be better to ask ...
1
vote
Heat map of protein expression from normalized abundance
The -2 to 2 should be the normalized version of log2 data (maybe mean or median normalization). This is commonly used in heatmaps to show downregulated value vs. upregulated value.
- 111
1
vote
Processing proteomics data
You asked two questions
Is it possible to find from the dataset (i.e does the raw file contain information on the sample whether it is a diabetic sample or a control sample?).
Should the diabetic and ...
M__♦
- 11.9k
1
vote
After completing the evaluation, how to predict PTM lysine or any other modification with unlabeled data for making a web server?
Interesting application. I would suggest using Python's Flask system, which is described in a few pages in O'Reilly's Programming PyTorch, chapter 8. PyTorch in Production. Django is not really ...
M__♦
- 11.9k
1
vote
Accepted
How to match peptide sequence from two different condition
merge(a, b, by = "Sequence") would "merge" the two tables (as the name suggests) based on the Sequence ...
- 3,947
1
vote
Holistic enzyme activity determination with computation
Your title says holistic. This is a tad problematic as there's layers upon layers. Say, post-translation regulation, inhibiting metabolites, interacting protein etc....
- 4,234
1
vote
Accepted
What unit is the length of a protein measured in?
As mentioned by others, it's the number of amino acids. Alternative measurements could be in Angstroms or similar, but that would require at least an approximate structure.
- 19.6k
1
vote
How identifiable are human omics data and how to mitigate their identifying features?
PPK provides a great answer, but for question 2 I can provide a different perspective. For shotgun metagenome sequencing (without any enrichment/depletion protocols) it is common for >90% of reads ...
- 3,928
1
vote
Accepted
How to download multiple proteomes at once?
You could try download-refseq-genomes. It will fetch all genomes from the NCBI FTP server that are in a specific subtree of the phylogeny.
For example, downloading the amino acid sequences from all ...
- 443
1
vote
Accepted
How to map selected genes to Metabolic pathway Maps
KEGG has a webtool for this, KEGG Mapper.
You can just copy-paste your gene ids in there and see how your pathways are colored.
- 3,571
1
vote
Why does a missing label 11plex TMT shows up at almost 50% intensity compared to other labels?
The developers answered along these lines:
This might be a normalization artefact. Reporter is normalizing the ratios so that the median is 1. So, if the label is almost not present the noise gets ...
- 1,295
Only top scored, non community-wiki answers of a minimum length are eligible