Generic workflow for quality assessment of quantitative label-free LC-MS analysis

Research output: Contribution to journalArticle

Standard

Generic workflow for quality assessment of quantitative label-free LC-MS analysis. / Sandin, Marianne; Krogh, Morten; Hansson, Karin M; Levander, Fredrik.

In: Proteomics, Vol. 11, No. 6, 2011, p. 1114-1124.

Research output: Contribution to journalArticle

Harvard

APA

CBE

MLA

Vancouver

Author

Sandin, Marianne ; Krogh, Morten ; Hansson, Karin M ; Levander, Fredrik. / Generic workflow for quality assessment of quantitative label-free LC-MS analysis. In: Proteomics. 2011 ; Vol. 11, No. 6. pp. 1114-1124.

RIS

TY - JOUR

T1 - Generic workflow for quality assessment of quantitative label-free LC-MS analysis

AU - Sandin, Marianne

AU - Krogh, Morten

AU - Hansson, Karin M

AU - Levander, Fredrik

PY - 2011

Y1 - 2011

N2 - As high resolution instruments are becoming standard in proteomics laboratories, label-free quantification using precursor measurements is becoming a viable option, and is consequently rapidly gaining popularity. Several software solutions have been presented for label-free analysis, but to our knowledge no conclusive studies regarding the sensitivity and reliability of each step of the analysis procedure has been described. Here we use real complex samples to assess the reliability of label-free quantification using four different software solutions. A generic approach to quality test quantitative label-free LC-MS is introduced. Measures for evaluation are defined for feature detection, alignment and quantification. All steps of the analysis could be considered adequately performed by the utilized software solutions, although differences and possibilities for improvement could be identified. The described method provides an effective testing procedure, which can help the user to quickly pinpoint where in the workflow changes are needed.

AB - As high resolution instruments are becoming standard in proteomics laboratories, label-free quantification using precursor measurements is becoming a viable option, and is consequently rapidly gaining popularity. Several software solutions have been presented for label-free analysis, but to our knowledge no conclusive studies regarding the sensitivity and reliability of each step of the analysis procedure has been described. Here we use real complex samples to assess the reliability of label-free quantification using four different software solutions. A generic approach to quality test quantitative label-free LC-MS is introduced. Measures for evaluation are defined for feature detection, alignment and quantification. All steps of the analysis could be considered adequately performed by the utilized software solutions, although differences and possibilities for improvement could be identified. The described method provides an effective testing procedure, which can help the user to quickly pinpoint where in the workflow changes are needed.

KW - quality control

KW - LC-MS

KW - label-free quantification

U2 - 10.1002/pmic.201000493

DO - 10.1002/pmic.201000493

M3 - Article

VL - 11

SP - 1114

EP - 1124

JO - Proteomics

T2 - Proteomics

JF - Proteomics

SN - 1615-9861

IS - 6

ER -