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.

Schenk et al. BMC Medical Genomics 2008 1:41   doi:10.1186/1755-8794-1-41

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