TMT -labeling quantification

[spoudel77]

Hi,

I have interact.pep.xml and interact.prot.xml and when I wanted to perform label quantification, it gives me an error. INFO[09:13:07] Executing Isobaric-label quantification v2.1.1 FATA[09:13:07] Cannot read file:open .meta/ev.param.bin: no such file or directory

Has anyone seen this before?

I have annotation.txt file sig126 S1 sig127N S2 sig127C S3 sig128N S4 sig128C S5 sig129N S6 sig129C S7 sig130N S8 sig130C S9 sig131N S10 sig131C S11

The code used is

!/bin/bash

set -xe

dataDirPath="/research/projects/penggrp/psychENCODE/penggrp/software_dev/PTM_study/ThermoRawFile_Test_NeuronData/TestSet"

annotFile="/research/projects/penggrp/psychENCODE/penggrp/software_dev/PTM_study/annotation.txt"

$philosopherPath workspace --clean $philosopherPath workspace --init $philosopherPath labelquant --annot $annotFile --plex 11 --dir $dataDirPath

$philosopherPath report $philosopherPath workspace --clean

Thank you for the help.

Sincerely, Suresh

[prvst]

@spoudel77

I see two different issues here, 1) there are some steps missing from your script and 2) your annotation file is not using the standard Thermo label names. I advise you to carefully read our documentation, specially the TMT analysis tutorial.

[spoudel77]

Thank you. I didn't keep rest of the script. I just kept the script that had problem. I will check the annotation file, only thing the document says tell Philosopher what sample is in each TMT channel. I will try with real sample name.

[spoudel77]

Thanks Felipe for the suggestion. I had only one error. sig126 S1 sig127N S2 sig127C S3 sig128N S4 sig128C S5 sig129N S6 sig129C S7 sig130N S8 sig130C S9 sig131N S10 sig131C S11

should be

126 S1 127N S2 127C S3 128N S4 128C S5 129N S6 129C S7 130N S8 130C S9 131N S10 131C S11

I got my output files