Questions tagged [proteomics]

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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 ...
Omar Shehab's user avatar
2 votes
0 answers
139 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 ...
Alicia's user avatar
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running fragpipe

I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
Mahendra Singh's user avatar
1 vote
1 answer
36 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 ...
Yifan Wang's user avatar
1 vote
1 answer
79 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 ...
Mary Allen's user avatar
2 votes
1 answer
153 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 ...
Kelly's user avatar
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2 votes
1 answer
38 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 ...
Adonis Cedeño's user avatar
1 vote
0 answers
22 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 ...
FalleS's user avatar
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1 vote
1 answer
70 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 ...
LJM's user avatar
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1 vote
1 answer
37 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 ...
Balasubramaniam Namasivayam's user avatar
0 votes
1 answer
36 views

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 ...
Natasha's user avatar
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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 ...
Natasha's user avatar
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2 votes
1 answer
911 views

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 ...
Natasha's user avatar
  • 125
2 votes
1 answer
92 views

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 ...
719016's user avatar
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3 votes
1 answer
412 views

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 ...
Natasha's user avatar
  • 125
1 vote
0 answers
19 views

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 ...
FrAoJm's user avatar
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1 vote
1 answer
55 views

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 ...
kcm's user avatar
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1 answer
27 views

How to match peptide sequence from two different condition

I have to peptide output sample output i would give here .. Sample A ...
kcm's user avatar
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1 vote
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68 views

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,...
phytofan's user avatar
1 vote
1 answer
131 views

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 ...
FJ_nw's user avatar
  • 11
-1 votes
1 answer
74 views

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 ...
Ehsan Salehabadi's user avatar
0 votes
1 answer
41 views

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 ...
ronald birb's user avatar
0 votes
1 answer
782 views

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. ...
icedcoffee's user avatar
1 vote
0 answers
24 views

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 ...
icedcoffee's user avatar
1 vote
1 answer
52 views

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?
Eliza Ganguly's user avatar
2 votes
1 answer
758 views

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 ...
Mee's user avatar
  • 81
0 votes
1 answer
165 views

How can I match sequences with IDs using python dictionaries?

...
Mike 's user avatar
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0 votes
2 answers
82 views

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, ...
clove444's user avatar
1 vote
0 answers
23 views

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-...
DN1's user avatar
  • 45
0 votes
0 answers
2k views

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 ...
Javan Okendo's user avatar
1 vote
1 answer
34 views

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 ...
Sabit Ahmed's user avatar
1 vote
2 answers
3k views

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 ...
Manuel's user avatar
  • 113
2 votes
2 answers
292 views

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 ...
Laura's user avatar
  • 881
1 vote
1 answer
39 views

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 ...
Dendrobium's user avatar
3 votes
1 answer
567 views

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 ...
Osaama Shehzad's user avatar
0 votes
2 answers
235 views

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 ...
iamakhilverma's user avatar
-1 votes
1 answer
78 views

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 ...
Angel's user avatar
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1 vote
0 answers
48 views

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 ...
Soerendip's user avatar
  • 1,295
0 votes
1 answer
178 views

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 ...
Badscience's user avatar
1 vote
1 answer
829 views

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 ...
Soerendip's user avatar
  • 1,295
1 vote
0 answers
24 views

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 ...
Soerendip's user avatar
  • 1,295
3 votes
1 answer
71 views

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 ...
Soerendip's user avatar
  • 1,295
1 vote
0 answers
144 views

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 ...
Soerendip's user avatar
  • 1,295
4 votes
2 answers
106 views

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 ...
Whateversclever's user avatar
4 votes
2 answers
2k views

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? ...
Kynda's user avatar
  • 95
5 votes
1 answer
472 views

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) ...
Dendrobium's user avatar