A high confidence, manually validated human blood plasma protein reference set

BMC Medical Genomics

Table 1 Plasma experiments performed.

Experiment	Designated name	Plasma treatment	[Protein] (μg) applied	Plasma separation method	MS	LC-MS run time/sample (minutes)	Comment
Plasma_01	01_MS2	none	450	1-D PAGE	MS/MS2	100
Plasma_04	04_MS2_prec	none	750	1-D PAGE	MS/MS2	100	Precursor selection within certain mass ranges only
Plasma_05	05	none	750	1-D PAGE	MS/MS2/MS3	100
Plasma_06	06_Alb_depl	Albumin-depletion	1800	1-D PAGE	MS/MS2/MS3	100
Plasma_10	10_Alb_depl _NL	Albumin depletion, Protease inhibitors	1800	1-D PAGE	MS/MS2/MS3	100	Neutral loss dependent MS3
Plasma_08	08_OGE	none	1800	OGE	MS/MS2/MS3	140
Plasma_09	09_OGE_6_depl	Depletion of albumin, transferrin, haptoglobin, alpha-1-antitrypsin, IgA and IgG	650	OGE	MS/MS2/MS3	140
Plasma_11	11_Orbitrap	Depletion of albumin, transferrin, haptoglobin, alpha-1-antitrypsin, IgA and IgG	300	1-D PAGE	MS/MS2	140

A summary of the differences in the experimental protocols between plasma experiments is shown. Each experiment has been assigned a meaningful "designated name" that is used in the text and in the accompanying figures and tables. Note that all experiments include MS3 measurements with the exception of 01_MS2, 04_MS2_prec and 11_Orbitrap. The type of treatment performed on the plasma samples, if any, is indicated, along with the amount of material applied to the gel, the separation method employed, and the method used for MS data collection.

ISSN: 1755-8794