Systematic Assessment of Survey
Scan and MS2-Based
Abundance Strategies for Label-Free Quantitative Proteomics Using
High-Resolution MS Data
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Abstract
Survey-scan-based label-free method
have shown no compelling benefit
over fragment ion (MS2)-based approaches when low-resolution mass
spectrometry (MS) was used, the growing prevalence of high-resolution
analyzers may have changed the game. This necessitates an updated,
comparative investigation of these approaches for data acquired by
high-resolution MS. Here, we compared survey scan-based (ion current,
IC) and MS2-based abundance features including spectral-count (SpC)
and MS2 total-ion-current (MS2-TIC), for quantitative analysis using
various high-resolution LC/MS data sets. Key discoveries include:
(i) study with seven different biological data sets revealed only
IC achieved high reproducibility for lower-abundance proteins; (ii)
evaluation with 5-replicate analyses of a yeast sample showed IC provided
much higher quantitative precision and lower missing data; (iii) IC,
SpC, and MS2-TIC all showed good quantitative linearity (<i>R</i><sup>2</sup> > 0.99) over a >1000-fold concentration range;
(iv)
both MS2-TIC and IC showed good linear response to various protein
loading amounts but not SpC; (v) quantification using a well-characterized
CPTAC data set showed that IC exhibited markedly higher quantitative
accuracy, higher sensitivity, and lower false-positives/false-negatives
than both SpC and MS2-TIC. Therefore, IC achieved an overall superior
performance than the MS2-based strategies in terms of reproducibility,
missing data, quantitative dynamic range, quantitative accuracy, and
biomarker discovery