Mass error ppm for peptides and modifications

[Daryl Wilding-McBride]

Hello, and thank you for sharing this software.

Am I correct in thinking that MSstats.csv contains all peptides and modifications found by identification or matching between runs? Is there a way of knowing whether a peptide was found with MBR?

For all peptides and modifications identified in technical replicates with MBR on, I'm interested in the delta ppm of the observed mass from the theoretical. Is the mass delta for all peptides and modifications reported, whether or not they are found by MBR? Do I need output_format = tsv_pepXML?

Best regards,
Daryl.

[Fengchao]

Hi Daryl,

Am I correct in thinking that MSstats.csv contains all peptides and modifications found by identification or matching between runs?

Yes.

Is there a way of knowing whether a peptide was found with MBR?

In peptide.tsv and ion.tsv files, those with 0 spectral count are from MBR.

For all peptides and modifications identified in technical replicates with MBR on, I'm interested in the delta ppm of the observed mass from the theoretical. Is the mass delta for all peptides and modifications reported, whether or not they are found by MBR?

There are PSM-level delta mass which is from MS/MS matching. The delta mass from MBR is not reported. Please note that both of the delta masses are from the mass error between the observed one and theoretical one, there is no unknown modification included, because MBR won't work with open search.

Best,

Fengchao

[Daryl Wilding-McBride]

Thanks Fengchao, that's helpful.