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The dried sample was dissolved in 50 µl of 50 mM formic acid/75% isopropanol and applied to polyhydroxyethyl A 10-µl solid phase extraction tip (Glygen Corporation, Columbia, MD).
In other experiments, the tryptic peptides from five 25-ml cultures were adjusted to pH 2.8 by the addition of 10% formic acid and applied to a Polysulfoethyl A 10-µl solid phase extraction tip (Glygen Corporation).
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Our approach provides an alternative to off-line extraction tips (with typical capacities of 1 2 μg and sample volumes of 1 10 μL), and to on-chip efforts based on packed bed and frit formats using a standard material for MEMs and standard microfabrication techniques.
Peptides in the immunoprecipitation eluate (40 µl) were concentrated and separated from eluted antibody using Stop and Go extraction tips (StageTips) [65].
Protein digestion was performed as described previously (Shevchenko et al., 1996) and peptides were desalted and concentrated using miniaturized micro-extraction tips (Rappsilber et al., 2003).
Following digestion, peptides were desalted using C18STop And Go Extraction (STAGE) tips (made "in-house") [19].
Peptide digests were purified using the C18 flavor of STop And Go Extraction (STAGE) tips [46] and eluted peptides were dried and labelled by reductive dimethylation using formaldehyde isotopologues [22], [47].
Fractions eluted from the SCX column were desalted with C18 Empore (3 M, Minneapolis, MN, USA) stop and go extraction (STAGE) tips [54] and subsequently subjected to nano-flow RP-HPLC using the Ultimate LC system (Dionex) equipped with a nanoflow calibration cartridge at a flow rate of 250 nL/min.
Eluted peptides were dried under vacuum before being loaded onto in-house packed C18 stop and go extraction (STAGE) tips.
Ten micrograms of digested peptides were purified with STop And Go Extraction (STAGE) tips [ 55] and labelled via reductive dimethylation using formaldehyde isotopologues [ 56, 57].
The protein digest was desalted with SPEC-PTC18 solid phase extraction pipette tips (Varian Inc., Lake Forest, CA, USA), concentrated to ~4 mg/mL, and stored at -80°C prior to further analysis.
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