The proteomics dataset in picture for this analysis is from Target ALS. First attempt to analyze the dataset which include 224 plasma raw files and 198 csf raw files separately.

SDRF file creation #

Due to the large amount of files and since its is a TMT experiment too, a script was used to make the sdrf file

The columns used for the file

 1COLS = [
 2    'source name',
 3    'characteristics[organism]',
 4    'characteristics[organism part]',
 5    'characteristics[age]',
 6    'characteristics[sex]',
 7    'characteristics[cell type]',
 8    'characteristics[cell line]',
 9    'characteristics[disease]',
10    'characteristics[depletion]',
11    'characteristics[developmental stage]',
12    'characteristics[individual]',
13    'characteristics[pooled sample]',
14    'characteristics[biological replicate]',
15    'assay name',
16    'technology type',
17    'comment[technical replicate]',
18    'comment[data file]',
19    'comment[file uri]',
20    'comment[fraction identifier]',
21    'comment[label]',
22    'comment[instrument]',
23    'comment[proteomics data acquisition method]',
24    'comment[dissociation method]',
25    'comment[modification parameters]',
26    'comment[modification parameters]',
27    'comment[modification parameters]',
28    'comment[modification parameters]',
29    'comment[cleavage agent details]',
30    'comment[precursor mass tolerance]',
31    'comment[fragment mass tolerance]',
32    'comment[sdrf version]',
33    'comment[sdrf template]',
34    'factor value[disease]',
35]

Modification columns used the following

1MOD_PARAMS = [
2    'NT=TMTpro;AC=UNIMOD:2016;PP=Any N-term;MT=Fixed',
3    'NT=TMTpro;AC=UNIMOD:2016;TA=K;MT=Fixed',
4    'NT=Carbamidomethyl;AC=UNIMOD:4;TA=C;MT=Fixed',
5    'NT=Oxidation;AC=UNIMOD:35;TA=M;MT=Variable',
6]

Beyond that, the following are the other acquisition constants

1INSTRUMENT   = 'NT=Orbitrap Eclipse;AC=MS:1003028'
2ACQ_METHOD   = 'Data-Dependent Acquisition'
3DISSOCIATION = 'AC=MS:1000422;NT=HCD'
4PREC_TOL     = '10 ppm'
5FRAG_TOL     = '0.02 Da'

In factor value column Norm is used for pooled rows.

The database utilized was the current bersion at the time of the uniprot human swissprot fasta database in combination with a potential contaminant database.

Analysis run #

I ran into a problem due to the usage of TMT35plex in the original experiment with the additional deuterium channels and it seemed at the time that quantms currently support maximum TMT18plex and PRIDE does not have the ontology terms for the new deuterium channels. To make it work, I stripped the sdrf tables of any row with deuterium channels.

last updated: 2026-08-09