In-Depth Profiling of the Peripheral Blood Mononuclear Cells Proteome for Clinical Blood Proteomics

Table 1

Summary of all LC-MS runs depicting the applied fractionation and liquid chromatography, as well as MS method (standard is referring to the description in Section 2).

LC-MS run	Fractionation method	LC method	MS method
2 h LC HCD 1	No	5–30% ACN over 90 minutes	Standard
2 h LC HCD exclusion list	No	5–30% ACN over 90 minutes	Exclusion list
2 h LC HCD 2	No	5–30% ACN over 90 minutes	Standard
2 h LC HCD 3	No	5–30% ACN over 90 minutes	Standard
2 h LC HCD 4	No	5–30% ACN over 90 minutes	Standard
2 h LC HCD 5	No	5–30% ACN over 90 minutes	Standard
2 h LC HCD (m/z 300–1500) 1	No	5–30% ACN over 90 minutes	m/z 300–1500
2 h LC HCD (m/z 300–1500) 2	No	5–30% ACN over 90 minutes	m/z 300–1501
2 h LC HCD (m/z 300–1500) 3	No	5–30% ACN over 90 minutes	m/z 300–1502
2 h LC HCD (m/z 300–1500) 4	No	5–30% ACN over 90 minutes	m/z 300–1503
2 h LC HCD (m/z 300–536)	No	5–30% ACN over 90 minutes	m/z 300–536
2 h LC HCD (m/z 531–679)	No	5–30% ACN over 90 minutes	m/z 531–679
2 h LC HCD (m/z 674–840)	No	5–30% ACN over 90 minutes	m/z 674–840
2 h LC HCD (m/z 835–1500)	No	5–30% ACN over 90 minutes	m/z 835–1500
4 h LC HCD 1	No	5–30% ACN over 215 minutes	Standard
4 h LC HCD 2	No	5–30% ACN over 215 minutes	Standard
6 h LC HCD 1	No	5–30% ACN over 335 minutes	Standard
6 h LC HCD 2	No	5–30% ACN over 335 minutes	Standard
8 h LC HCD 1	No	5–30% ACN over 455 minutes	Standard
8 h LC HCD 2	No	5–30% ACN over 455 minutes	Standard
SCX fraction 1 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 2 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 3 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 4 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 5 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 6 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 7 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 8 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 9 2 h LC HCD	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 1 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 2 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 3 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 4 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 5 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 6 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 7 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 8 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 9 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 10 2 h LC HCD exclusion list	SCX chromatography	5–30% ACN over 90 minutes	Exclusion list
SCX fraction 1 2 h LC (15–30% ACN)-optimized LC gradient	SCX chromatography	15–30% ACN over 90 minutes	Standard
SCX fraction 2 2 h LC (15–30% ACN)-optimized LC gradient	SCX chromatography	15–30% ACN over 90 minutes	Standard
SCX fraction 3 2 h LC (5–30% ACN)-optimized LC gradient	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 4 2 h LC (0–30% ACN)-optimized LC gradient	SCX chromatography	0–30% ACN over 90 minutes	Standard
SCX fraction 5 2 h LC (0–30% ACN)-optimized LC gradient	SCX chromatography	0–30% ACN over 90 minutes	Standard
SCX fraction 6 2 h LC (5–30% ACN)-optimized LC gradient	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 7 2 h LC (10–30% ACN)-optimized LC gradient	SCX chromatography	10–30% ACN over 90 minutes	Standard
SCX fraction 8 2 h LC (5–30% ACN)-optimized LC gradient	SCX chromatography	5–30% ACN over 90 minutes	Standard
SCX fraction 9 2 h LC (0–30% ACN)-optimized LC gradient	SCX chromatography	0–30% ACN over 90 minutes	Standard
SCX fraction 10 4 h LC (5–30% ACN)-optimized LC gradient	SCX chromatography	5–30% ACN over 215 minutes	Standard