Re: Channel names for MaxQuant MSstatsTMT

[thuan...@gmail.com]

Hi,

Is it possible to share a subset of your evidence file? Currently, it is hard to know the reason since we are unable to reproduce the error on our laptop.

Best,

Ting

On Wednesday, October 13, 2021 at 11:08:05 AM UTC-4 t.h.st...@lumc.nl wrote:

Hi there,

I'm struggling to find out why I get:

error in .mergeAnnotation(input, annotation) : 

  ** Please check the annotation file. The channel name must be matched with that in input data.

I've included my annotation file (conditions are replaced with x).

My evidence file has the exact same columns names, but my proteinGroups file has an additional nummer (for the 3 different mixtures used).

Thanks in advance!

[Nikhil]

Hello,

I am getting the same error. Wasn't happening when I was using packages from CRAN, but recently installed them from github and it's refusing to merge. I have tried variations of channel names including just the numbers, "Channel.x", "Channel x" and ".x", but all return the same result. Could you please help?

Thanks!

-Nikhil

[Mateusz Staniak]

Hi,

please try channelx or channel.x. We will make this column (and others) case-insensitive in the nearest future.

Kind regards,

Mateusz

[Nikhil]

Yes, that worked. Thanks!

[debor...@gmail.com]

Hi Mateusz,

I am facing the same problem, but using  channelx or channel.x did not work for me. What should I do?

Thank you

Best,

Debora

[Mateusz Staniak]

Hi,

please post column names of input data and unique values of Channel column of annotation. This should be enough to identify the issue.

Kind regards,

Mateusz

[debor...@gmail.com]

Hi Mateusz,

Thank you so much!

Here is the column name of my input data:

 Evidence:
Sequence
Length
Modifications
Modified sequence
Deamidation (NQ) Probabilities
Oxidation (M) Probabilities
Deamidation (NQ) Score Diffs
Oxidation (M) Score Diffs
Deamidation (NQ)
Oxidation (M)
Missed cleavages
Proteins
Leading proteins
Leading razor protein
Type
Raw file
Fraction
Experiment
MS/MS m/z
Charge
m/z
Mass
Uncalibrated - Calibrated m/z [ppm]
Uncalibrated - Calibrated m/z [Da]
Mass error [ppm]
Mass error [Da]
Uncalibrated mass error [ppm]
Uncalibrated mass error [Da]
Max intensity m/z 0
Retention time
Retention length
Calibrated retention time
Calibrated retention time start
Calibrated retention time finish
Retention time calibration
Match time difference
Match m/z difference
Match q-value
Match score
Number of data points
Number of scans
Number of isotopic peaks
PIF
Fraction of total spectrum
Base peak fraction
PEP
MS/MS count
MS/MS scan number
MS/MS scan numbers
MS3 scan numbers
Score
Delta score
Combinatorics
Intensity
Reporter intensity corrected 1
Reporter intensity corrected 2
Reporter intensity 1
Reporter intensity 2
Reporter intensity count 1
Reporter intensity count 2
Reverse
Potential contaminant
id
Protein group IDs
Peptide ID
Mod. peptide ID
MS/MS IDs
Best MS/MS
Deamidation (NQ) site IDs
Oxidation (M) site IDs
Taxonomy IDs
Mass deficit

proteinGroups:

Protein IDs
Majority protein IDs
Peptide counts (all)
Peptide counts (razor+unique)
Peptide counts (unique)
Fasta headers
Number of proteins
Peptides
Razor + unique peptides
Unique peptides
Peptides Cytosol _R1
Peptides Cytosol_R2
Peptides Cytosol_R3
Peptides Nucleo_R1
Peptides Nucleo_R2
Peptides Nucleo_R3
Razor + unique peptides Cytosol _R1
Razor + unique peptides Cytosol_R2
Razor + unique peptides Cytosol_R3
Razor + unique peptides Nucleo_R1
Razor + unique peptides Nucleo_R2
Razor + unique peptides Nucleo_R3
Unique peptides Cytosol _R1
Unique peptides Cytosol_R2
Unique peptides Cytosol_R3
Unique peptides Nucleo_R1
Unique peptides Nucleo_R2
Unique peptides Nucleo_R3
Sequence coverage [%]
Unique + razor sequence coverage [%]
Unique sequence coverage [%]
Mol. weight [kDa]
Sequence length
Sequence lengths
Fraction average
Fraction 1
Fraction 2
Q-value
Score
Identification type Cytosol _R1
Identification type Cytosol_R2
Identification type Cytosol_R3
Identification type Nucleo_R1
Identification type Nucleo_R2
Identification type Nucleo_R3
Reporter intensity corrected 1 Cytosol _R1
Reporter intensity corrected 2 Cytosol _R1
Reporter intensity corrected 1 Cytosol_R2
Reporter intensity corrected 2 Cytosol_R2
Reporter intensity corrected 1 Cytosol_R3
Reporter intensity corrected 2 Cytosol_R3
Reporter intensity corrected 1 Nucleo_R1
Reporter intensity corrected 2 Nucleo_R1
Reporter intensity corrected 1 Nucleo_R2
Reporter intensity corrected 2 Nucleo_R2
Reporter intensity corrected 1 Nucleo_R3
Reporter intensity corrected 2 Nucleo_R3
Reporter intensity 1 Cytosol _R1
Reporter intensity 2 Cytosol _R1
Reporter intensity 1 Cytosol_R2
Reporter intensity 2 Cytosol_R2
Reporter intensity 1 Cytosol_R3
Reporter intensity 2 Cytosol_R3
Reporter intensity 1 Nucleo_R1
Reporter intensity 2 Nucleo_R1
Reporter intensity 1 Nucleo_R2
Reporter intensity 2 Nucleo_R2
Reporter intensity 1 Nucleo_R3
Reporter intensity 2 Nucleo_R3
Reporter intensity count 1 Cytosol _R1
Reporter intensity count 2 Cytosol _R1
Reporter intensity count 1 Cytosol_R2
Reporter intensity count 2 Cytosol_R2
Reporter intensity count 1 Cytosol_R3
Reporter intensity count 2 Cytosol_R3
Reporter intensity count 1 Nucleo_R1
Reporter intensity count 2 Nucleo_R1
Reporter intensity count 1 Nucleo_R2
Reporter intensity count 2 Nucleo_R2
Reporter intensity count 1 Nucleo_R3
Reporter intensity count 2 Nucleo_R3
Sequence coverage Cytosol _R1 [%]
Sequence coverage Cytosol_R2 [%]
Sequence coverage Cytosol_R3 [%]
Sequence coverage Nucleo_R1 [%]
Sequence coverage Nucleo_R2 [%]
Sequence coverage Nucleo_R3 [%]
Intensity
Intensity Cytosol _R1
Intensity Cytosol_R2
Intensity Cytosol_R3
Intensity Nucleo_R1
Intensity Nucleo_R2
Intensity Nucleo_R3
MS/MS count
Peptide sequences
Only identified by site
Reverse
Potential contaminant
id
Peptide IDs
Peptide is razor
Mod. peptide IDs
Evidence IDs
MS/MS IDs
Best MS/MS
Deamidation (NQ) site IDs
Oxidation (M) site IDs
Deamidation (NQ) site positions
Oxidation (M) site positions
Taxonomy IDs

Here is the data in the Channel column:

channel.1
channel.2
channel.3
channel.4
channel.5
channel.6
channel.7
channel.8
channel.9
channel.10

Thank you so much!

Best,
Debora

[Mateusz Staniak]

Hi,

the converter expects "Reporter intensity" columns in the evidence. Are you using a recent version of MaxQuant that possibly changed export options?

Kind regards,
Mateusz

[debor...@gmail.com]

Hi Mateusz!

Thank you so much!

I used Version 2.0.3.0 of maxquant. I will search again using another version to test this. 

Thank you so much!

Best,

Debora