Questions tagged [proteomics]
The proteomics tag has no usage guidance.
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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 ...
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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 ...
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Ensuring arbitrary cuttoffs don't bias dataset towards high intensity protiens
I have a TMT proteomic dataset with proteins all of which are in set A and some of pass a calculated cutoff, are differentially regulated between conditions and/or are signal peptide positive. Using ...
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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 ...
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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 ...
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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 ...
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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 ...
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Convert Mascot mztab file format to XML
Cross-posted here
I would like to convert MASCOT mztab file to XML format. I have been looking for converters and I came across PRIDE Converter but this is no longer available for download from here ...
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Setting up MaxQuant parameters for processing proteomics data
This is a follow up to my previous question here.
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes ...
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Heat map of protein expression from normalized abundance
This is a follow up to my question posted here
Processing proteomics data
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article ...
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De novo antibody sequencing fromMS/MS Ion Trap proteomics raw signal
I've read about different proteomics tools that can do de novo assembly of MS/MS Ion Trap proteomics signatures for de novo antibody sequencing. Given the way CDR3s of antibodies are created, together ...
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Processing proteomics data
[this question was also asked on BioStars]
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes marked ...
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method to compare the similarity between proteomic profiles
I have a problem finding a methodology to compare proteomic profiles against another. The experiment is the following:
Experiment 1. Ten pdx tumour models with their proteomic profiles were done in ...
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Peptide data visualization
I'm trying to replicate the figure given in this paper using this table which they have given.
So what i understand from the figure is they have calculated the zscore between two condition and ...
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How to match peptide sequence from two different condition
I have to peptide output sample output i would give here ..
Sample A
...
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Transcriptomics vs Proteomics for understanding molecular responses [closed]
I am planning some experiments to investigate how mono cultures of microbes respond to different nutrient concentrations. I want to use an -omics based approach to understand how, on a molecular level,...
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Help with DIA-Mass Spectrometry data analysis with several conditions (limma?)
I am trying to learn how to analyse normalised DIA-MS data and I am struggling with it ://
The original dataset I got is (6 conditions (2 samples each)) with 3 technical replicates (total: 36 sample ...
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A database for RefSeq protein accession IDs
Are there any databases or tools that contain a list of all RefSeq protein IDs for the interest organism/microorganism, e.g. get a specific microorganism name and return all RefSeq Protein IDs that ...
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Holistic enzyme activity determination with computation [closed]
I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
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What unit is the length of a protein measured in?
Sorry if this question is obvious - I'm not familiar with proteomics so I'm not sure of the standard units.
In this paper, it talks about using the length of a protein to calculate the NSAF value. ...
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How to calculate protein abundance from an .mzTab file?
I have an .mzTab file, with PRT and PSM values. Does anyone know of any specific functions that I could use to calculate protein abundance values from this data?
More details
This is a summary of ...
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Mapping protein refseq to Gene ID
I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?
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median normalization for proteomics
I am using the data from a proteomics study were the data was log2 transformed and then a median normalization was applied. The data was normalized by groups of conditions (normal, mutant), not for ...
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How identifiable are human omics data and how to mitigate their identifying features?
Say a database were to store human omics datasets. The human subjects are known and the sample size is rather small in size initially (n=500). The database contains genomics, transcriptomics, ...
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How do protein-protein interaction databases work?
I am a student and just trying to gain a base level understanding of PPI databases and how to interpret their data.
For example, when inputing multiple genes into String, does it only give protein-...
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Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ‘"SeqFastaAA"’ to a data.frame
The example that I am trying to follow is this PGA tutorial.
I want to use the information in the analysis of the mzML raw files from the proteomics data analysis.
When I try to load the fasta file, I ...
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After completing the evaluation, how to predict PTM lysine or any other modification with unlabeled data for making a web server?
I have created a model with SVM classifier and evaluated it with 5-fold cross-validation. The dataset was sequence data containing lysine modified sites. Now I want to build a web server where anyone ...
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Running MaxQuant on Linux
I'm trying to run MaxQuant on a linux laptop, hower I'm constantly running into problems with MaxQuant crashing at different stages
I tried to use
mono 6.8
mono 5.4.1
on
centos
ubuntu
each with ...
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How to download multiple proteomes at once?
I'm looking for a way to download multiple proteomes at once from one clade, as fasta. Probably from the NCBI, because it looks more user-friendly than Ensembl, but Ensembl is okay too. In the best ...
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How to map selected genes to Metabolic pathway Maps
I have a selected Arabidopsis Genome Initiative (AGI) list for RNA seq and proteomics data, how can I map them to metabolic pathway maps to vilualize(e.g. TCA cycle / FA / Photosynthesis) in KEGG or ...
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Principle of TMT Tags in Multiplex Proteomics
I am new to proteomics research and analyzing mass-spec data. I am trying to learn more about the theory/principle of TMT tagging (a type of isobaric labeling) coupled with LC-MS/MS spectrometry. I ...
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Proteomics data Vs Transcriptomics data?
I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
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How I normalize these two sets of data
I have average log fold change for a cluster of cells versus another cluster of cells by Seurat like below
...
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What is the purpose of the "fixedSearchFolder" and "fixedCombinedFolder" in MaxQuant?
What is the purpose of changing the fixedSearchFolder and fixedCombinedFolder in MaxQuant proteomics software? Is there any data ...
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Preparing PDB file for modeling with Swiss-Model
I recently starting studying bioinformatics and have a question. I need to build a model of protein using Swiss-Model. First, I need to download a protein record from PDB (for example, 2HZI), then I ...
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What is the purpose of 'Folder locations' in MaxQuant?
MaxQuant is a tool for proteomics quantification. In the settings under Global parameters / Folder locations are three folder locations that are possible to be ...
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Can MSstatsTMT be used for both MS2 and MS3 runs?
MSstatsTMT is an R library for statistical analysis of TMT labeled mass-spectrometry (MS) proteomics data. The documentation does not explicitly mention the kind of MS that can be processed. The ...
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Why does a missing label 11plex TMT shows up at almost 50% intensity compared to other labels?
We have a test plate that was done with 10 of the 11plex TMT labels. So, the intensities of the 11th label should be almost zero, plus the leakage from the 10th label due to 13C content. Although we ...
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How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?
I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
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Block wise protein imputation
I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The features of the date set are:
The data is perfectly balanced between blocks, with equal treatment ...
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Omics data: How to interpret heatmap and dendrogram output?
How to interpret heat map and dendrogram output for biological data (omics) in words (when writing results and discussion)?
What should I consider (statistics behind?) and what is the best approach?
...
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How to interpret PCA output statistically and biologically?
How can I interpret the PCA results statistically for biological data?
I have used FactoMineR and factoextra libraries for PCA
Scripts used:
library(FactoMineR)
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