MaxQuant 2.0.3.0 is not reporting iBAQ values?

More Sebastian Hoernstein's questions See All

Questions about granite analysis using remote sensing?

I am studying large-scale granite structures, specifically inselbergs. I would like to know your suggestions for analyzing these granite structures using remote sensing. Books, articles, and...

17 June 2024 6,687 1 View

¿Existen Investigaciones en torno a la Geopolítica Precolonial en Latinoamerica?

Me encuentro realizando una investigación sobre La Historia del Comercio Internacional de Colombia, En el Primer capítulo me encuentro abordando los imperios Latinoamericanos precoloniales como el...

21 March 2024 4,148 2 View

What are the possible scales to measure perceived legal risk in an organizational context?

I am looking for scales to measure the perceptions of legal risk when developing certain software or information system features.

14 March 2024 7,854 2 View

Is it required to send interview transcriptions for publishing qualitative research in a journal as part of data availability?

As someone engaging in ethnographic research, are we expected to disclose transcribed data to the journal where we would like publish an article?

03 March 2024 3,653 3 View

In the context of VIGS. What reasons can cause the failing to culture/grow Agrobacterium in LB media?

Hello. I am trying to culture Agrobacterium GV 3103 and EHA105 in 15 mL LB media with the antibiotics kanamycin and rifampicin (100 ug/mL & 20 ug/mL)(added 200 uL of previously normally...

25 January 2024 812 5 View

What does it mean if I have STD signals from a protein sample without a ligand?

While performing STD screening I noticed that I have signals in my difference spectras, that are constant accross all samples, also if there is no ligand and only protein. The protein was...

18 January 2024 6,932 2 View

What is the difference between a chelating resin and an IMAC resin containing IDA? Is that the latter has already immobilized a metal?

I cannot see the difference between these two types of resins that contain iminodiacetic acid as functional groups besides that the IMAC resins contain the metal for the His-tag. Is this the only...

14 January 2024 8,378 5 View

Looking for alternatives: More affordable Capillaries?

Dear fellow lab rats. In our lab, we are using the original capillaries from Nanotemp for their machines. We use it to let the protein solution Panta run through them or the Protein-Ligand...

02 January 2024 8,391 0 View

I would like to work on complementary SRR. How to simulate CSRR using HFSS/ CST?

16 December 2023 1,658 1 View

How to convert DNA copies per microliter to nanogram per microliter in the context of absolute DNA quantification?

DD PCR

28 November 2023 1,895 2 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 do I open maxquant file?

I previously processed proteomics LC-MS/Ms raw files with maxquant. Through this, I obtained sec files including msms scan and PTM identification, and files with the results displayed in txt also....

16 April 2024 583 0 View

Can MaxQuant be set up to detect sodium ionisation of peptides?

Due to factors outside of my control, peptides in my ESI-MS data have been ionised normally by protons ([M+2H], [M+3H]...) but also by sodium ([M+2Na], [M+3Na]...). Is there a way to configure...

16 April 2024 10,028 2 View

MaxQuant is throwing a configuring error, can someone help me figure out what it means?

I am running MaxQuant and it starts running and almost immediately stops. I go into the error folder (combined-->proc, then select Configuring 11.error). The screenshot of the error is...

14 February 2024 6,348 1 View

Why do I have low peptide identification (% of MS/MS identified is around 0)?

Dear all, I have performed an IP in cell lysate with a trypsin digest, have run the samples of a QE mass spectrometer and now performed a maxquant search against the human proteome (v2.1.3.0)...

12 February 2024 2,761 6 View

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

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...

15 January 2024 1,081 1 View

LFQ intensities missing from peptides txt file?

I'm running MQ on some peptide-level enrichment TurboID samples, so I'm interested in quantifying individual peptides. In past versions of Maxquant (v1.6.14 etc), the peptides.txt file contained...

02 January 2024 3,158 5 View

Why the detected protein count reduced when i perfomed proteomics of 30 .raw files and then 100 .raw (prev. 30 files included) using maxquant?

Recently i started a proteomics of blood plasma (100 ms/ms files .raw) against fungal fasta (from uniprot) using MaxQuant in linux. I started with 6 .raw then 30 and finally all 100 files. In 6...

02 January 2024 3,171 5 View

Has anyone already used GPT4 for OMICs data analysis?

Looking for somebody to share experience on using ChatGPT 4 as an assisting tool (in combination with either Excel or Perseus MaxQuant) for analyzing data such as OMICs. Concretely I'm dealing...

29 November 2023 3,962 2 View

Why does my volcano plot have the shape on an anchor?

I am performing shotgun proteomics, using MaxQuant and Perseus for analysis. When I used imputation from a normal distribution to fill in invalid values I end up getting a normal looking volcano...

10 September 2023 3,318 5 View

Nils Rugen

Hi Sebastian,

do you get no iBAQs at all or is it just not working for all of your proteins?

Best,

Nils

Sebastian Hoernstein

unfortunately I don´t get iBAQ values for any protein....

Maybe database problem?

What Database do you use? Something custom?

And do you get any Peptide intensities in "peptides.txt"?

Hi,

yes it´s a custom database in fasta format. I get intensities in the peptide.txt file, also LFQ values are provided.

If anyone had the same problem, I found it. iBAQ does not work when semispecific protease specificity is chosen. Somewhat logic ....