Differential recovery of peptides from sample tubes and the reproducibility of quantitative proteomic data.

Differential recovery of peptides from sample tubes and the reproducibility of quantitative proteomic data.

Journal of proteome research (2007-09-14)

Steven J Bark, Vivian Hook

ABSTRACT

Differential recovery of peptides due to nonspecific adsorption can seriously compromise reproducibility and quality of proteomic data for peptide analyses by liquid chromatography-mass spectrometry (LC-MS). This study demonstrates large variations in reproducibility and quantitation of LC-MS data for peptides derived from tryptic digests of BSA upon storage in different sample tubes. Notably, we show that highly improved consistency and lower errors in quantitation of BSA tryptic peptides in replicate measurements is achieved with low-retention tubes compared to regular eppendorf tubes. Furthermore, qualitative differences in peptides detected by LC-MS were observed in the two types of storage tubes. These results illustrate the necessity for careful evaluation of storage vessels and conditions to minimize variability in sample quality for LC-MS experiments.

MATERIALS

Product Number

Brand

Product Description

EP951031607

Eppendorf^® Deepwell plates, DNA LoBind, 384 wells, white plate, conical bottom, colorless wells, capacity 200 μL, pack of 120 ea (10 bags × 12 plates)

EP022431021

Eppendorf^® DNA LoBind tubes, capacity 1.5 mL, PCR clean, pkg of 250 ea (5 x 50ea)

EP951031208

Eppendorf^® Deepwell plates, DNA LoBind, 384 wells, white plate, conical bottom, colorless wells, capacity 200 μL, pack of 40 ea (5 bags × 8 plates)

EP951032883

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 1000 μL, pkg of 120 ea (10 bags × 12 plates)

EP022431005

Eppendorf^® DNA LoBind tubes, capacity 0.5 mL, PCR clean, pkg of 250 ea (5 x 50ea)

EP951032085

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 40 ea (5 bags × 8 plates)

EP022431048

Eppendorf^® DNA LoBind tubes, capacity 2.0 mL, PCR clean, pkg of 250 ea (5 x 50ea)

EP951032000

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 40 ea (5 bags × 8 plates)

EP951032409

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 120 ea (10 bags × 12 plates)

EP951032808

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 1000 μL, pkg of 120 ea (10 bags × 12 plates)

EP951033201

Eppendorf^® Deepwell plates, DNA LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 1000 μL, pkg of 80 ea (10 bags × 8 plates)

EP951040601

Eppendorf^® Protein LoBind Microplate 384/V-PP, PCR clean, V-bottom clear wells, white border, pack of 240 ea (10 bags × 24 plates)

EP951032921

Eppendorf^® Deepwell plates, Protein LoBind, 96 wells, yellow plate, conical bottom, colorless wells, capacity 500 μL, pkg of 20 ea (5 bags × 4 plates)

EP951032123

Eppendorf^® Deepwell plates, Protein LoBind, 96 wells, yellow plate, conical bottom, colorless wells, capacity 500 μL, pkg of 40 ea (5 bags × 8 plates)

EP951033308

Eppendorf^® Deepwell plates, Protein LoBind, 96 wells, white plate, conical bottom, colorless wells, capacity 500 μL, pkg of 80 ea (10 bags × 8 plates)

EP022431064

Eppendorf^® Protein LoBind tubes, capacity 0.5 mL, PCR clean, pkg of 100 ea (2 x 50ea)

EP022431081

Eppendorf^® Protein LoBind tubes, capacity 1.5 mL, PCR clean, pkg of 100 ea (2 x 50ea)

EP022431102

Eppendorf^® Protein LoBind tubes, capacity 2.0 mL, PCR clean, pkg of 100 ea (2 x 50ea)