I have been investigating the data reported for this experiments and the metadata is incomplete (the pHs are absent but they are present in the article and in comments of info.tsv) and, apart from that, the list of metabolites reported in supplementary information contain a name and they have RTs that are later not present in the processed data. It looks there are 3 different chromatographic conditions (RP pos with pH 3.0 in mobile phase A, RP neg with pH 8.0 in mobile phase A, and HILIC) in the reported identifications and there are 3 different columns described in the manuscript:
"
Three different columns were investigated: 2.1 × 150 mm, 2.5 μm T3 Xselect column HSS XP (Waters),
2.1 × 100 mm, 2.7 μm Express C18 column (Ascentis) and
2.1 × 100 mm, 2.7 μm Express F5 column (Ascentis). The flow rate on
each column was 300 μl/min heated at 40 °C. For positive ionization
mode, mobile phase A was 5 mM ammonium formate in water with an
adjusted pH of 3.0 by the addition of formic acid, and mobile phase B
was methanol. For negative ionization mode, mobile phase C was 5 mM
ammonium acetate in water with an adjusted pH of 8.0 by the addition
of ammonium hydroxide. The gradient used in positive mode was
0–1 min, 5% B; 1–20 min, 5–95% B; 20–25 min, 95% B; 25–28 min, 5%
B. In negative mode, mobile phase C was used instead of mobile phase
A. The injection volume was 1 μl for the urine samples and 1–10 μl for
the reference compounds. Samples were cooled at 6 °C. The dead volume was 1.0 min for the 150 mm Waters column and 0.6 min for the
two 100 mm Ascentis columns.
"
However, there are 3 datasets containing RTs and two of them contain the same chromatographic conditions. I am happy to help filling the info but in this case I would need to see or develop the scripts to obtain data and adapt it to your standard repoRT info. Please let me know how we can proceed :)
I have been investigating the data reported for this experiments and the metadata is incomplete (the pHs are absent but they are present in the article and in comments of info.tsv) and, apart from that, the list of metabolites reported in supplementary information contain a name and they have RTs that are later not present in the processed data. It looks there are 3 different chromatographic conditions (RP pos with pH 3.0 in mobile phase A, RP neg with pH 8.0 in mobile phase A, and HILIC) in the reported identifications and there are 3 different columns described in the manuscript:
"
Three different columns were investigated: 2.1 × 150 mm, 2.5 μm T3 Xselect column HSS XP (Waters),
2.1 × 100 mm, 2.7 μm Express C18 column (Ascentis) and
2.1 × 100 mm, 2.7 μm Express F5 column (Ascentis). The flow rate on
each column was 300 μl/min heated at 40 °C. For positive ionization
mode, mobile phase A was 5 mM ammonium formate in water with an
adjusted pH of 3.0 by the addition of formic acid, and mobile phase B
was methanol. For negative ionization mode, mobile phase C was 5 mM
ammonium acetate in water with an adjusted pH of 8.0 by the addition
of ammonium hydroxide. The gradient used in positive mode was
0–1 min, 5% B; 1–20 min, 5–95% B; 20–25 min, 95% B; 25–28 min, 5%
B. In negative mode, mobile phase C was used instead of mobile phase
A. The injection volume was 1 μl for the urine samples and 1–10 μl for
the reference compounds. Samples were cooled at 6 °C. The dead volume was 1.0 min for the 150 mm Waters column and 0.6 min for the
two 100 mm Ascentis columns.
"
However, there are 3 datasets containing RTs and two of them contain the same chromatographic conditions. I am happy to help filling the info but in this case I would need to see or develop the scripts to obtain data and adapt it to your standard repoRT info. Please let me know how we can proceed :)