Upcoming Backwards-Incompatible Changes in MSstats 3.21 – Action Required

[Anthony Wu]

If you do not directly use the MSstatsSummarize function in MSstats or the groupComparisonPTM function in MSstatsPTM, you can ignore this note.

We are introducing backwards-incompatible changes in the upcoming MSstats 3.21 bioconductor release.

1. Deprecation of MSstatsSummarize: This function will be replaced by MSstatsSummarizeWithMultipleCores for improved performance.  See this example for details on how to use this function for protein summarization.

2. Changes to groupComparisonPTM Parameters: The data.type parameter will be replaced by two new parameters: ptm_label_type and protein_label_type. This change allows group comparisons in MSstatsPTM when the label type differs between PTM and proteome-wide datasets (e.g., TMT for PTM and label-free for proteome-wide).  To ensure backwards compatibility for existing workflows, take the value used for data.type and set that value for  both ptm_label_type and protein_label_type.
   

If you have questions or need clarification, please reply to this post.

Thanks,

Tony  

[Anthony Wu]

Correction: MSstatsSummarize will be replaced in favor of MSstatsSummarizeWithSingleCore