The present disclosure relates to ALK, Ros, Ron, Ret, TS, and / or in biological samples immobilized in formalin by a method also referred to as selective reaction monitoring (SRM) mass spectrometry, or multiple reaction monitoring (MRM) mass spectrometry. Alternatively, it provides specific peptides derived from ALK, Ros, Ron, Ret, TS, and / or FGFR1 proteins that are particularly advantageous for direct quantification of FGFR1 protein, and derived ionization properties of those peptides. Such biological samples are chemically stored and fixed, the biological sample comprising formalin fixed tissues / cells, formalin fixed / paraffin embedded (FFPE) tissues / cells, FFPE tissue blocks and cells derived from those blocks, As well as tissues and cells treated with formaldehyde-containing drugs / fixants, including formalin-fixed and / or paraffin-embedded tissue culture cells. Protein samples are prepared from biological samples using Liquid Tissue ™ reagents and protocols, and ALK, Ros, Ron, Ret, TS, and / or FGFR1 proteins in Liquid Tissue ™ samples are SRM / MRM. By mass spectrometry, it is quantified by quantifying at least one or more of the described peptides in the protein sample. If these peptides are present in modified or unmodified form, they can be quantified. An example of a modified form of an ALK, Ros, Ron, Ret, TS, and / or FGFR1 fragment peptide is the phosphorylation of tyrosine, threonine, serine, and / or other amino acid residues in the peptide sequence It is.本開示は、選択反応モニタリング（ＳＲＭ）質量分析、または多重反応モニタリング（ＭＲＭ）質量分析とも称される方法によってホルマリン中で固定された生体試料中のＡＬＫ、Ｒｏｓ、Ｒｏｎ、Ｒｅｔ、ＴＳ、及び／またはＦＧＦＲ１タンパク質を直接定量化するのに特に有利なＡＬＫ、Ｒｏｓ、Ｒｏｎ、Ｒｅｔ、ＴＳ、及び／またはＦＧＦＲ１タンパク質由来の特異的ペプチド、及びそれらのペプチドの派生イオン化特性を提供する。そのような生体試料は、化学的に保存及び固定され、該生体試料は、ホルマリン固定組織／細胞、ホルマリン固定／パラフィン包埋（ＦＦＰＥ）組織／細胞、ＦＦＰＥ組織ブロック及びそれらのブロック由来の細胞、ならびにホルマリン固定及び／またはパラフィン包埋された組織培養細胞を含む、ホルムアルデヒド含有薬剤／固定剤で処理された組織及び細胞から選択される。タンパク質試料は、Ｌｉｑｕｉｄ Ｔｉｓｓｕｅ（商標）試薬及びプロトコルを使用して生体試料から調製され、Ｌｉｑｕｉｄ Ｔｉｓｓｕｅ（商標）試料中のＡＬＫ、Ｒｏｓ、Ｒｏｎ、Ｒｅｔ、ＴＳ、及び／またはＦＧＦＲ１タンパク質は、ＳＲＭ／ＭＲＭ質量分析法により、タ
