difficulties in creating annotation.pd

[me37uday]

Hey,

I am trying to create the annotation.pd file and I needed some help understanding a certain things. So the experimental design is as follows :

There were 27 human post-mortem tissues from the dorsolateral prefrontal cortex, which were digested and labeled with 3 batches of 11 plex TMT reagents. Two pooled global internal standards (GIS) were labeled with channels 126 and 131 C in each batch. There were 9 samples from 3 groups (control, AsymAD and AD) randomized and labeled in the remainder channels. The labeled sample mixture was fractionated by off-line high-pH reversed-phase chromatography into 24 fractions. All fractions were analyzed on an Orbitrap Fusion Lumos Tribrid mass spectrometer.

Sample trait file is as contained in the attached file : sampletraits.xlsx

The raw files are co-analysed (specified as fractions in PD) to produce a single PSM.csv. How many rows and what should the columns of annotation.pd be?

Uday