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Samples were analyzed using a gradient described previously [6].
Standards and Siliphos capsule extracts were analyzed using a gradient from 30:70 to 55 45 methanol:water (0.1% formic acid) over 5.0 minutes at a flow rate of 0.6 ml/minute at 50 °C; peaks were detected at 288 nm.
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Samples were analyzed using a linear gradient (0% to 50% B, from 0 to 4 min; 50% to 100% B, from 4 to 4.50 min and then kept at 100% B to 5 min).
The first 10 fractions from SCX were analyzed using an 88 min gradient and the next 11 fractions were analyzed using a 55 min gradient, since the first 10 fractions had greater sample complexity, allowing for more peptide identifications (data not shown).
Protein mix samples were analyzed using a 110 min chromatography gradient, whereas HeLa samples were analyzed using a 3.5 h chromatography gradient and gas-phase fractionation.
These samples were analyzed using an LC gradient from 2 to 70% acetonitrile in 120 minutes.
Gradients were analyzed using a WellChrom Filter-Photometer K-2001UV and Brandel top collecting pump system at OD254.
40 μL of the resulting solution were analyzed using a Shimadzu Mass Spectrometer LC-MS 2020 (gradient: 20 to 80% acetonitrile with 0.1% formic acid over 8 min).
Raw data was analyzed using a custom-written computer code in the R-environment (see http://www.r-project.org/), which removed a linear background gradient.
Cells were analyzed using a BD FACSCalibur.
Data were analyzed using a Matlab program.
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