MaxQuant intensities missing from "modification".txt file in the txt folder ?

16 January 2024 1 1K Report

I have run MaxQuant in LFQ mode, and it seems that some of the variable modification specified in the specific-group parameters are displaying an intensity of 0 despite the protein/peptide has been listed in the "modification.txt" document. I have also tried running iBAQ mode and that didn't seem to solve the problem. When checking the proteingroup,txt the protein has been assigned with an intensity. Any idea why the protein could be listed in the modification.txt without having a value ?

Thanks

Murat Eravci

Hi Ibtissam,

did you defined the mentioned variable modifications in global parameters/protein quantification tab (peptides for quantification)?

Best,

Murat

More Ibtissam mustapha Jabre's questions See All

How to model a phase change material on Comsol Multiphysics?

I am looking for the steps to model the behavior of a phase change material (PCM) on Comsol Multiphysics. The tutorials on YouTube are not useful for me. I model PCM on ansys Fluent, but I...

10 January 2023 4,242 1 View

Does anyone have an idea about polymer flooding, or chemical enhanced oil recovery, the addition of nanoparticules on the injected solution ?

more details about the effect of concentration, temperature, salinity and hardness on apparent viscosity

28 July 2021 8,323 5 View

How to have the equation of a curve on excel correctly?

Hello I would to have an udf that presentes the evolution of the daily radiation (by collecting the x and y (of a curve of an article for validation) from the "GET DATA"). At First, I drew my...

11 April 2019 7,679 5 View

Dear researchers, can you help me in the design of a MLP Neural Network applied to a Doubly Fed Induction Generator ?

I want to control the Wind Energy Conversion System based on DFIG with MLPNN, but I don't know what the inputs and outputs of my neural network would be.? and if you can help with any other...

16 March 2018 3,851 6 View

What is the best model to evaluate the antibacterial activity in vivo?

For exemple in sepsis model some researchers use intravenous inoculation and others intraperitoneal.

03 February 2018 9,120 6 View

Hi everyone, how can i choose FLC gains to have a reduced response time?

Actually i'm working on a wind system, now i want to replace the PI controller with Fuzzy Logic Controller for MPPT strategy, but i have a problem defining the right gains to obtain some good results.

12 April 2017 9,543 4 View

Trajectory of minors migrants

what do you think about the trajectory of minors migrants into Europe ?

01 January 1970 507 4 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

Unusual intensity drop in some sections of chromatograms in DDA?

Hi, we have measured tryptic peptides using both DDA and DIA method on QExactive. In DDA replicates i saw unusual intensity drops occurring at the same sections of chromatograms in DDA replicates...

07 August 2024 3,218 4 View

How to analyze multiple phosphorilation sites?

Hello, I am currently analyzing some phosphoproteomics data, but I have peptides with multiple phosphorylation sites or phosphorylations together with carbamidomethylation or oxidation. How can I...

04 August 2024 8,432 3 View

Recovery rate after peptide desalting using Sep-pack C18 1 cc Vac Cartridge?

Recently I'm trying to use Sep-pack C18 1 cc Vac Cartridge (Waters: SKU: WAT054955) to desalt digested peptides. However, the recovery rate is usually 40-60%. What is the normal recovery rate?

31 July 2024 6,544 11 View

Is it possible to conjugate an NHS ester to the N-terminus of a peptide ON RESIN?

So i have a few peptides (synthesized by SPPS and not cleaved from resin) and I want to add a maleimide label. We have NHS-PEG-Maleimide and from literature it is evident that the free amine group...

18 July 2024 4,075 3 View

Does sucrose interfere with the BCA reagent in peptide concentration assays?

Hello everyone! I am currently working on the expression and purification of an antimicrobial peptide that experiences reduced activity after each freeze-thaw cycle. To improve its stability, I...

10 July 2024 6,830 1 View

What strains of C57 mice can induce rheumatoid arthritis?

Recently I looked up a literature《A Glucose-6-Phosphate Isomerase Peptide Induces T and BCell-Dependent Chronic Arthritis in C57BL/10 Mice Arthritis without Reactive Oxygen Species and...

09 July 2024 6,657 0 View

I found trouble to run MD of my peptide with PTM in different force field. In Charm-GUI, it cant recognize the engineering residue. What can I do now?

I am working on my PTM project. I have some peptide. I got the result of doing MD of those peptide without PTM in different force field like Charm-GUI, Amber, Gromacs. Now I have to do MD of those...

05 July 2024 9,346 0 View

How "MaxQuant" can recognize my Mass Spectrometry data?

Dear all, I am writing to explain my problem and would greatly appreciate any small hints that might help alleviate my desperation. I am relatively new to proteomics, and our laboratory has an old...

26 June 2024 9,948 10 View

How to prepare a transparent solution of the peptide with the mixture of hydrophobic and hydrophilic amino acids ?

I am using a peptide and have faced challenges in preparing a transparent peptide solution. My goal is to prepare a peptide solution in MES buffer and then use the solution to immobilize the...

20 June 2024 8,622 5 View