Supplementary Datasets 1–11.

Supplementary Dataset 1: Proteins identified by combined analysis of replicates for each of the ten protocols of the study Supplementary Dataset 2: Peptides and proteins identified by individual analysis of each replicate for the FASP, Amicon 10k protocol Supplementary Dataset 3: Peptides and proteins identified by individual analysis of each replicate for the FASP, Amicon 30k protocol Supplementary Dataset 4: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, Amicon 10k, phase transfer protocol Supplementary Dataset 5: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, Amicon 10k, precipitation protocol Supplementary Dataset 6: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, passivated Amicon 10k, phase transfer protocol Supplementary Dataset 7: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, passivated Amicon 10k, precipitation protocol Supplementary Dataset 8: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, Amicon 30k, phase transfer protocol Supplementary Dataset 9: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, Amicon 30k, precipitation protocol Supplementary Dataset 10: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, passivated Amicon 30k, phase transfer protocol Supplementary Dataset 11: Peptides and proteins identified by individual analysis of each replicate for the Amicon-adapted eFASP, passivated Amicon 30k, precipitation protocol