A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments

Robert Moulder, Jan-Jonas Filén, Jussi Salmi, Mikko Katajamaa, Olli S. Nevalainen, Matej Oresic, Tero Aittokallio, Riitta Lahesmaa, Tuula A. Nyman

Research output: Contribution to journalArticleScientificpeer-review

23 Citations (Scopus)

Abstract

The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR® Pulsar quadrupole‐TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.
Original languageEnglish
Pages (from-to)2748 - 2760
Number of pages13
JournalProteomics
Volume5
Issue number11
DOIs
Publication statusPublished - 2005
MoE publication typeA1 Journal article-refereed

Fingerprint

Liquid chromatography
Tandem Mass Spectrometry
Liquid Chromatography
Isotopes
Mass spectrometry
Software
Experiments
DEAE-Dextran
Peptides
Proteins
Mass spectrometers
Processing
Software packages
Mass Spectrometry
Productivity
Cytokines
Light
Datasets

Keywords

  • Isotope coded affinity tag
  • Protein quantification
  • Software evaluation
  • Tandem mass spectrometry

Cite this

Moulder, Robert ; Filén, Jan-Jonas ; Salmi, Jussi ; Katajamaa, Mikko ; Nevalainen, Olli S. ; Oresic, Matej ; Aittokallio, Tero ; Lahesmaa, Riitta ; Nyman, Tuula A. / A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. In: Proteomics. 2005 ; Vol. 5, No. 11. pp. 2748 - 2760.
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Moulder, R, Filén, J-J, Salmi, J, Katajamaa, M, Nevalainen, OS, Oresic, M, Aittokallio, T, Lahesmaa, R & Nyman, TA 2005, 'A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments', Proteomics, vol. 5, no. 11, pp. 2748 - 2760. https://doi.org/10.1002/pmic.200401187

A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments. / Moulder, Robert; Filén, Jan-Jonas; Salmi, Jussi; Katajamaa, Mikko; Nevalainen, Olli S.; Oresic, Matej; Aittokallio, Tero; Lahesmaa, Riitta; Nyman, Tuula A.

In: Proteomics, Vol. 5, No. 11, 2005, p. 2748 - 2760.

Research output: Contribution to journalArticleScientificpeer-review

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T1 - A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments

AU - Moulder, Robert

AU - Filén, Jan-Jonas

AU - Salmi, Jussi

AU - Katajamaa, Mikko

AU - Nevalainen, Olli S.

AU - Oresic, Matej

AU - Aittokallio, Tero

AU - Lahesmaa, Riitta

AU - Nyman, Tuula A.

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N2 - The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR® Pulsar quadrupole‐TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.

AB - The options available for processing quantitative data from isotope coded affinity tag (ICAT) experiments have mostly been confined to software specific to the instrument of acquisition. However, recent developments with data format conversion have subsequently increased such processing opportunities. In the present study, data sets from ICAT experiments, analysed with liquid chromatography/tandem mass spectrometry (MS/MS), using an Applied Biosystems QSTAR® Pulsar quadrupole‐TOF mass spectrometer, were processed in triplicate using separate mass spectrometry software packages. The programs Pro ICAT, Spectrum Mill and SEQUEST with XPRESS were employed. Attention was paid towards the extent of common identification and agreement of quantitative results, with additional interest in the flexibility and productivity of these programs. The comparisons were made with data from the analysis of a specifically prepared test mixture, nine proteins at a range of relative concentration ratios from 0.1 to 10 (light to heavy labelled forms), as a known control, and data selected from an ICAT study involving the measurement of cytokine induced protein expression in human lymphoblasts, as an applied example. Dissimilarities were detected in peptide identification that reflected how the associated scoring parameters favoured information from the MS/MS data sets. Accordingly, there were differences in the numbers of peptides and protein identifications, although from these it was apparent that both confirmatory and complementary information was present. In the quantitative results from the three programs, no statistically significant differences were observed.

KW - Isotope coded affinity tag

KW - Protein quantification

KW - Software evaluation

KW - Tandem mass spectrometry

U2 - 10.1002/pmic.200401187

DO - 10.1002/pmic.200401187

M3 - Article

VL - 5

SP - 2748

EP - 2760

JO - Proteomics

JF - Proteomics

SN - 1615-9853

IS - 11

ER -