How to use the code to analysis the data search from tair?

[manni227]

Code:
library(MSstatsPTM)
library(MSstats)
library(data.table)

path_pro <- "/Users/PRO_1.tsv"
path_phos <- "/Users/PHOS_2.tsv"
path_fasta <- "/Users?TAIR10_pep.txt"

raw_ptm_df <- fread(path_phos)
raw_protein_df <- fread(path_pro)

ptm_proteins <- unique(raw_ptm_df$PG.ProteinAccessions)
raw_protein_df <- raw_protein_df[PG.ProteinAccessions %in% ptm_proteins, ]

raw_ptm_df[is.na(R.Replicate) | R.Replicate == "" | R.Replicate == 0, R.Replicate := R.FileName]
raw_protein_df[is.na(R.Replicate) | R.Replicate == "" | R.Replicate == 0, R.Replicate := R.FileName]

gc()

annot <- unique(rbind(
raw_ptm_df[, .(Run = R.FileName, Condition = R.Condition, BioReplicate = R.Replicate)],
raw_protein_df[, .(Run = R.FileName, Condition = R.Condition, BioReplicate = R.Replicate)]
))

msstats_input <- SpectronauttoMSstatsPTMFormat(
raw_ptm_df,
annotation = annot,
protein_input = raw_protein_df,
fasta_path = path_fasta,
use_unmod_peptides = TRUE,
mod_id = "\[Phospho \(STY\)\]",
fasta_protein_name = "uniprot_iso"
)

Error in [.data.table(data, , c(protein_name_col, unmod_pep_col, mod_pep_col, :
column not found: [Start]

PRO_1.tsv
TAIR10_pep.txt
PHOS_1.tsv

[tonywu1999]

Hi @manni227

To assist us, can you provide a link to a uniprot entry for your protein of interest in your dataset (e.g. AT1G01050.1)? And did you download this FASTA via uniprot or somewhere else?

If you run:

path_fasta <- "/Users?TAIR10_pep.txt"
fasta_df = MSstatsPTM::tidyFasta(path_fasta)

You'll see that the code parses the FASTA file such that AT1G01050.1 corresponds to the uniprot ID T1G010, which I believe is incorrect (but would need confirmation of the uniprot entry to make the code fix).

[tonywu1999]

@manni227

If you need more help, could you start a conversation on our msstats google groups page? We check that google groups page more periodically.

[manni227]

Hi @tonywu1999 I am so sorry for not checking in time.Thank you so much for your answer. I am not sure if i know what should i need to provide. The entry of At4g08850 in uniprot is Q8VZG8. The entry of AT1G01050.1 in uniprot is Q93V56 The entry of AT5G47910 in uniprot is Q9FIJ0. tonywu1999 ***@***.***> 于2026年1月14日周三 22:05写道：

…

*tonywu1999* left a comment (Vitek-Lab/MSstatsPTM#122) <#122 (comment)> Hi @manni227 <https://github.com/manni227> To assist us, can you provide a link to a uniprot entry for your protein of interest in your dataset (e.g. AT1G01050.1)? If you run: path_fasta <- "/Users?TAIR10_pep.txt" fasta_df = MSstatsPTM::tidyFasta(path_fasta) You'll see that the code parses the FASTA such that AT1G01050.1 corresponds to the uniprot ID T1G010, which I believe is incorrect (but would need confirmation of the uniprot entry to make the code fix). — Reply to this email directly, view it on GitHub <#122 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWTPHNPFUE3GLY7KAS657XT4GZEMFAVCNFSM6AAAAACRQ73EQ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONBZG4YTSMBZG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>