Questions tagged [proteomics]
The proteomics tag has no summary.
51 questions
1 vote
0 answers
21 views
BioID SAINT downstream analysis
I have SAINT results which contain 2 types of baits CCER2-C and CCER2-N. I need to determine proteins which interact with CCER2-C vs CCER2-N. I have come across heat maps and dot plots by Prohits-viz ...
- 205
0 votes
0 answers
42 views
Looking for proteins play role in cardiovascular diseases (disease ontology)
I'm looking for proteins that (probaly) play role in cardiovascular diseases. I have to do a list about them. It's recommended to use The Disease Ontology. But if I'm correct this specific protein ...
2 votes
0 answers
36 views
Accuracy of large peptide fragment in LC-MS/MS
Peptide digestion leads to generation of small peptides (ideal) as well as some large peptides (3-4kDa). The large peptides often don't fly well and therefore do not detect well. Does it affect the ...
- 141
1 vote
2 answers
288 views
Fragment mass tolerance in proteomics analysis
Proteomics newbie here. I am using proteome discoverer software to analyze the fragmentation of a chemically modified single protein. In my understanding, when we set the Fragment mass tolerance to ...
- 141
1 vote
0 answers
87 views
Energy error margin for protein structures
I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their ...
- 111
2 votes
0 answers
583 views
How to perform PCA on proteomic data set
I'm trying to perform Principal Component Analysis using R on a proteomics dataset. As the dataset contains a lot missing values I tried different approaches. I ran PCA using ...
- 21
0 votes
0 answers
319 views
running fragpipe
I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
1 vote
1 answer
105 views
Handling duplicates in untargeted lipidomics
I have a MS-lipidomics dataset - from human samples split into a treatment group (n = 2) and control (n = 2) - which contains several detected targets that matched to the same lipid. I don't have ...
- 11
1 vote
1 answer
123 views
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?
I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same ...
- 31
2 votes
1 answer
365 views
Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?
I am new to proteomics analysis, so apologies if my question is silly! For context, I am working with proteome samples from the postmortem human brain for a case-control study. Our lab generally ...
- 21
2 votes
1 answer
72 views
Reduce Overfit by removing insignificant proteins through PSEA analysis
I'm training a ML model for disease prediction using protein composition as input, but overfit is present. While looking to remove proteins and reduce multi-correlation, as remove composition ...
1 vote
0 answers
34 views
Mass spectrometry: How to obtain expression counts for protein
I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent. Each sample corresponds to a folder ...
- 11
1 vote
2 answers
141 views
Advise on building an effect ML model for predicting important proteins for drug response
I want to create a model to predict proteins which could be associated with drug response in cancer cell lines. I have cell line proteomics data, with compound screening data they have gained for a ...
- 11
1 vote
1 answer
54 views
Gene/protein expression specific to a group in omics
I am wondering what is the significance of finding a particular protein specific to a disease or control group? when we detect 1000s of proteins in a proteomics experiment, how can one be sure that ...
0 votes
1 answer
89 views
Can Bioinformatics be used in developing a marketable product? [closed]
As we all know computer science, electrical engineering, etc. knowhows can be used in developing software and electronics/electrical products that can be sold to end-users (B2C). Can bioinformatics be ...
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